Phage therapy: An alternative to antibiotics in the age of multi-drug resistance

Peptides rapidly transport antibiotic across the intact tympanic membrane to treat a middle ear infection

The tympanic membrane (TM) forms an impenetrable barrier to medical therapies for middle ear (ME) diseases like otitis media. By screening a phage-displayed peptide library, we have previously discovered rare peptides that mediate the active transport of cargo across the intact membrane of animals and humans. Since the M13 filamentous bacteriophage on which the peptides are expressed are large (nearly 1 µm in length), this offers the possibility of noninvasively delivering drugs, large drug packages, or gene therapy to the ME. To evaluate this possibility, EDC chemistry was employed to covalently attach amoxicillin, or neomycin molecules to phage bearing a trans-TM peptide, as a model for large drug packages. Eight hours after application of antibiotic-phage to the TM of infected rats, ME bacterial titers were substantially reduced compared to untreated animals. As a control, antibiotic was linked to wild-type phage, not bearing any peptide, and application to the TM did not affect ME bacteria. The results support the ability of rare peptides to actively deliver pharmacologically relevant amounts of drugs through the intact TM and into the ME. Moreover, since bacteriophage engineered to express peptides are viral vectors, the trans-TM peptides could also transport other viral vectors into the ME.

Unveiling the potential bacteriophage therapy: a systematic review

INTRODUCTION

Antimicrobial resistance renders conventional therapy, demanding the need for alternative therapeutic techniques. A potential strategy for treating infections caused by multi-drug-resistant bacteria is using bacteriophages, viruses that only multiply and infect specific bacteria. This review aims to evaluate the findings of clinical studies on phage therapy for bacterial illnesses.

METHODS

A comprehensive search method was utilized to identify 11 appropriate trials, which were then assessed for safety, efficacy, and treatment outcomes. The Joann-Briggs-Institute checklist and PRISMA criteria were used to evaluate these studies thoroughly. The results were summarized by extracting and analyzing data on trial design, treatment outcomes, safety profiles, and therapeutic effectiveness.

RESULTS

Phage treatment had a strong safety profile, with few side effects recorded across many routes, including oral, intravenous, and topical. Clinical studies demonstrated its effectiveness in lowering bacterial loads, resolving infections, and destroying biofilms. However, diversity in trial designs hampered the generalizability of the findings.

CONCLUSION

This study emphasizes the promise of phage therapy as a safe and efficient treatment for bacterial-illnesses. Despite its potential, there are still significant gaps in clinical application, long-term efficacy assessment, and trial standardization. Addressing these issues is critical to developing phage therapy as an effective alternative treatment for multidrug-resistant-illnesses.

Targeting breast cancer: the promise of phage-based nanomedicines

BACKGROUND

Breast cancer is a leading cause of cancer-related mortality among women worldwide, characterized by its aggressive nature, propensity for metastasis, and resistance to standard treatment modalities. Traditional therapies, including surgery, chemotherapy, and radiation, often encounter significant limitations such as systemic toxicity and lack of specificity.

OBJECTIVE

This review aims to evaluate the recent advancements in phage-based nanomedicines as a novel approach for targeted breast cancer therapy, focusing on their mechanisms of action, therapeutic benefits, and the challenges faced in clinical implementation.

METHODS

A comprehensive literature review was conducted, analyzing studies that investigate the application of bacteriophages in cancer therapy, particularly in breast cancer. The review highlights the integration of nanotechnology with phage therapy, examining the potential for enhanced targeting and reduced side effects.

RESULTS

Phage-based nanomedicines have shown promise in selectively targeting breast cancer cells while sparing healthy tissues, thereby improving therapeutic efficacy and safety profiles. The unique properties of bacteriophages, including their ability to be engineered for specific targeting and their natural ability to induce immune responses, present significant advantages over conventional treatments.

CONCLUSION

The integration of phage therapy with nanotechnology represents a promising frontier in the fight against breast cancer. This review underscores the need for continued research to address existing challenges and to explore the full potential of phage-based nanomedicines in improving patient outcomes in breast cancer treatment.

Whole genome sequencing of the novel polyvalent bacteriophage Malk1: A powerful biocontrol agent for water pollution

In this study, a novel Malk1 phage, was isolated and characterized for its ability to target a broad range of multidrug-resistant (MDR) bacterial strains. Malk1, classified within the Siphoviridae family, showed lytic activity with a capsid diameter of 84 nm and a tail length of 205 nm. It demonstrated a short latent period of 18 min and a burst size of 102 virions per infected cell. The phage exhibited strong thermal stability up to 60 °C and maintained activity across a pH range of 6.0-10.0. However, exposure to hand soap and 70 % ethanol reduced its titers by over 94 % and 97 %, respectively. Malk1 lysed 92 % of the tested bacterial strains and had a genome of 44.3 kb, encoding 75 open reading frames (ORFs), with no genes for toxins, antibiotic resistance, or CRISPR elements, making it a virulent phage. A novel design utilizing immobilized polyvalent Malk1 phage on plastic sheets demonstrated superior efficacy in reducing multi-drug resistant (MDR) bacterial strains. The removal efficiencies for C.freundii (78-91 %), E.coli (74-85 %), S.enterica (60-76 %), and S.flexneri (63-72 %) were significantly higher compared to purified phage, which achieved removal efficiencies of 63-69 %, 58-66 %, 52-63 %, and 55-68 %, respectively, after 6 to 8 h. Furthermore, the immobilized phage treatment led to a 94.1 % improvement in the removal of physicochemical pollutants in wastewater, significantly surpassing the 65.3 % removal achieved with purified phage. The treatment process led to significant improvements in water quality, achieving an average removal efficiency of 71.1 % for electrical conductivity, 67.52 % for turbidity, 73.67 % for total dissolved solids (TDS), 88.02 % for biochemical oxygen demand (BOD), and 81.88 % for ammonia (NH₃). Additionally, the average dissolved oxygen (DO) levels increased by 79.17 % compared to untreated wastewater. These findings highlight the promising potential of Malk1 phage, particularly in its immobilized form, for pathogen control and enhancing water quality. ORIGINALITY-SIGNIFICANCE STATEMENT: We introduce the newly isolated polyvalent Malk1 phage, which has been thoroughly genome characterized and annotated. Immobilized Malk1 phage has proven effective in controlling drainage water pollution and addressing global concerns for irrigation water quality. Our experiments successfully reduced several multi-drug-resistant (MDR) bacterial strains in highly polluted drainage water, leading to significant improvements in water quality in a short time and at an affordable cost, facilitated by our innovative laboratory design.

Application of phage-derived enzymes for enhancing food safety

Foodborne pathogens such as Salmonella, Escherichia coli, Listeria monocytogenes, and Staphylococcus aureus present significant public health threats, causing widespread illness and economic loss. Contaminated food is responsible for an estimated 600 million illnesses and 420,000 deaths annually, with low- and middle-income countries facing losses of approximately $110 billion each year. Traditional methods to ensure food safety, including antimicrobials and preservatives, can contribute to the development of antimicrobial-resistant bacteria, highlighting the need for alternative strategies. Bacteriophages are gaining renewed attention as promising alternatives to conventional antibiotics due to their specifically target bacteria and their lower potential for causing adverse effects. However, their practical application is limited by challenges such as narrow host ranges, the emergence of phage-resistant bacteria, and stability issues. Recent research has shifted focus towards phage-derived enzymes, including endolysins, depolymerases, holins, and spanins, which are involved in the phage lytic cycle. These enzymes, as potential approaches to food safety, have demonstrated significant efficacy in targeting and lysing bacterial pathogens, making them suitable for controlling foodborne pathogens and preventing foodborne illnesses. Phage-derived enzymes also show promise in controlling biofilms and enhancing antimicrobial activity when combined with other antimicrobials. Therefore, this review emphasizes recent advancements in the use of the phage-derived enzymes for food safety, addresses their limitations, and suggests strategies to enhance their effectiveness in food processing and storage environments.

Characterization of novel phages KPAФ1, KP149Ф1, and KP149Ф2 for lytic efficiency against clinical MDR Klebsiella pneumoniae infections

Phage therapy offers a promising approach to the increasing antimicrobial resistance of Klebsiella pneumoniae. This study highlights three novel lytic bacteriophages-KPAФ1, KP149Ф1, and KP149Ф2- targeting multidrug-resistant (MDR) K. pneumoniae. These phages belong to the Myoviridae and Podoviridae family and demonstrate their efficacy and stability across a wide range of temperatures (up to 60°C) and pH levels (pH 4 to 11). Genomic analysis reveals that they are free from virulence, toxicity, and antimicrobial resistance genes, making them promising candidates for therapeutic use. Among these phages, KPAФ1 showed the highest lytic activity with a 26.15% lysis against MDR K. pneumoniae isolates. Additionally, a phage cocktail comprising all three phages improved lytic efficacy to 32.30%. This study also examined the antimicrobial resistance profiles of K. pneumoniae isolates, emphasizing the critical need for alternative treatments. By effectively targeting resistant strains, these phages offer a potential candidacy to be used as a viable alternative or a complementary antimicrobial agent to traditional antibiotics, opening up the possibility for advanced phage-based therapies. The promising results from this study pave the way for developing new treatments that could significantly improve patient care and outcomes from the growing issue of resistant bacterial infections.

Studies in vitro e in vivo of phage therapy medical products (PTMPs) Targeting Clinical Strains of Klebsiella pneumoniae belonging to the clone ST512

The widespread incidence of antimicrobial resistance has created renewed interest in the use of alternative antimicrobial treatments such as phage therapy. Phages are viruses that infect bacteria and generally have a narrow bacteria host-range. Combining phages with antibiotics can prevent the emergence of bacterial resistance. The aim of the present study was to develop phage therapy medical products (PTMPs) targeting clinical isolates of carbapenem-producing Klebsiella pneumoniae belonging to the high-risk clone ST512. From a collection of 22 seed of lytic phages sequenced belonging to MePRAM collection (Spanish Health Precision Medicine Project against Antimicrobial Resistance), four were used to generate PTMPs (CAC_Kpn1 and CAC_Kpn2). These PTMPs were partly active against three of the clinical strains of clone ST512 (A, B, and C). The use of Appelmans method in the CAC_Kpn1_ad (adapted CAC_Kpn1) yielded a significant increase in the efficacy against strain A, while adapted CAC_Kpn2 (CAC_Kpn2_ad) only effectively reduced bacterial survival when combined with ½ × MIC ß-lactam antibiotic meropenem for 24 h in clinical strains B and C, showed after this time, resistance to PTMPs. In addition, the amounts of endotoxin released by the PTMPs were quantified and subsequently reduced in preparation for in vivo use of the PTMPs in the Galleria mellonella infection model, confirming the in vitro results from the CAC_Kpn1_ad and CAC_Kpn2_ad. To sum up, the preparation of two PTMPs and their subsequent adaptation can be a good approach to solve part of the occurrence of antimicrobial resistance. In addition, the use of the larval model is an effective method to discriminate the efficacy of in vivo treatment.

Host-encoded DNA methyltransferases modify the epigenome and host tropism of invading phages

Restriction modification (RM) systems are ubiquitous bacterial defense systems; however, some phages evade RM system and adapt to their bacterial hosts. In such cases, phages are thought to stochastically acquire DNA methylation from host-encoded DNA methyltransferases (MTases), facilitating host adaptation. However, no studies have directly compared the methylomes of host bacteria and their infecting phages. Here, we demonstrate the epigenetic landscape of adapted phages with diverse infection histories, focusing on the broad host-range phage KHP30T as its adapts to three Helicobacter pylori strains. Using a multistage infection system, we observed that the adapted phages displayed significantly high titers against the last infected H. pylori strain, suggesting an attendant change in host tropism. Single-molecule real-time sequencing revealed that methylated motifs were predominantly shared between the adapted phages and their most recent host. Our findings enhance our understanding of epigenetic phage-host interactions, which have significant implications for microbial ecology.

Antimicrobial resistance: Linking molecular mechanisms to public health impact

BACKGROUND

Antimicrobial resistance (AMR) develops into a worldwide health emergency through genetic and biochemical adaptations which enable microorganisms to resist antimicrobial treatment. β-lactamases (blaNDM, blaKPC) and efflux pumps (MexAB-OprM) working with mobile genetic elements facilitate fast proliferation of multidrug-resistant (MDR) and exttreme drug-resistant (XDR) phenotypes thus creating major concerns for healthcare systems and community health as well as the agricultural sector.

OBJECTIVES

The review dissimilarly unifies molecular resistance pathways with public health implications through the study of epidemiological data and monitoring approaches and innovative therapeutic solutions. Previous studies separating their attention between molecular genetics and clinical outcomes have been combined into our approach which delivers an all-encompassing analysis of AMR.

KEY INSIGHTS

The report investigates the resistance mechanisms which feature enzymatic degradation and efflux pump overexpression together with target modification and horizontal gene transfer because these factors represent important contributors to present-day AMR developments. This review investigates AMR effects on hospital and community environments where it affects pathogens including MRSA, carbapenem-resistant Klebsiella pneumoniae, and drug-resistant Pseudomonas aeruginosa. This document explores modern AMR management methods that comprise WHO GLASS molecular surveillance systems and three innovative strategies such as CRISPR-modified genome editing and bacteriophage treatments along with antimicrobial peptides and artificial intelligence diagnostic tools.

CONCLUSION

The resolution of AMR needs complete scientific and global operational methods alongside state-of-the-art therapeutic approaches. Worldwide management of drug-resistant infection burden requires both enhanced infection prevention procedures with next-generation antimicrobial strategies to reduce cases effectively.

Optimizing phage therapy for carbapenem-resistant Enterobacter cloacae bacteremia: insights into dose and timing

The increase in multidrug-resistant (MDR) Enterobacter cloacae complex (ECC) infections, particularly those resistant to carbapenems, underscores the urgent need for alternative therapies. Phage therapy, with its specific bactericidal action, offers a promising solution. However, there remains a shortage of well-characterized ECC-targeting phages, and dosing and timing optimization for ECC-specific phage cocktails is largely unexplored. In this study, we isolated and characterized three novel lytic phages with diverse genome sizes and host ranges. Notably, ФEBU8 demonstrated broad-spectrum activity, lysing both Enterobacter species and Acinetobacter baumannii. ФECL22 displayed stability across a wide temperature range (4-50°C), pH tolerance (6-10), and a burst size of 19 PFU/cell, with OmpA identified as its receptor. Our formulated phage cocktail, comprising ФEBU8, ФECL22, and ФECL30, effectively rescued mice with E. cloacae bacteremia in a dose-dependent manner, with a mid-dose regimen showing particularly strong efficacy. Immediate phage administration achieved full survival, whereas a combined prophylactic and therapeutic regimen ("-24 + 6") also resulted in 100% survival. These findings highlight the critical roles of dosing and timing in optimizing phage therapy for carbapenem-resistant Enterobacter infections, with prophylactic use providing a valuable window for delayed treatment and a promising strategy for combating severe bacterial infections.

Novel nanomaterials-based combating strategies against drug-resistant bacteria

Numerous types of contemporary antibiotic treatment regimens have become ineffective with the increasing incidence of drug tolerance. As a result, it is pertinent to seek novel and innovative solutions such as antibacterial nanomaterials (NMs) for the prohibition and treatment of hazardous microbial infections. Unlike traditional antibiotics (e.g., penicillin and tetracycline), the unique physicochemical characteristics (e.g., size dependency) of NMs endow them with bacteriostatic and bactericidal potential. However, it is yet difficult to mechanistically predict or decipher the networks of molecular interaction (e.g., between NMs and the biological systems) and the subsequent immune responses. In light of such research gap, this review outlines various mechanisms accountable for the inception of drug tolerance in bacteria. It also delineates the primary factors governing the NMs-induced molecular mechanisms against microbes, specifically drug-resistant bacteria along with the various NM-based mechanisms of antibacterial activity. The review also explores future directions and prospects for NMs in combating drug-resistant bacteria, while addressing challenges to their commercial viability within the healthcare industry.

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.

Isolation, characterization, and genomic analysis of three novel Herelleviridae family lytic bacteriophages against uropathogenic isolates of Staphylococcus saprophyticus

BACKGROUND

Staphylococcus saprophyticus (S. saprophyticus) is the second most prevalent etiological agent of urinary tract infections (UTIs) in young women. However, there is a paucity of data regarding its bacteriophage (phage). Therefore, this study was conducted to isolate and identify new lytic phages from municipal wastewater with the objective of increasing knowledge about phages and their genomes.

METHODS

A total of 11 clinical isolates of S. saprophyticus and 30 wastewater samples were used to isolate three lytic phages (vB_SsapH-Golestan-100, vB_SsapH-Golestan101-M, and vB_SsapH-Golestan-105-M). The morphology, behavioral characteristics, and complete DNA genomes of these phages were analyzed.

RESULTS

The microscopic images of the phages revealed that the sizes of their heads and tail lengths fell within the ranges of 90-111 nm and 234-266 nm, respectively. All phages exhibited high adsorption rates (99.5% in 15 min) and burst sizes (150-210 PFU per infected cell), with a potential for a narrow host range. Genomic analysis of Staphylococcus phages indicated a size of 136,433 base pairs (bp) with a guanine-cytosine (GC) content of 33.7% and 192 open reading frames (ORFs) for vB_SsapH-Golestan-100, 144,081 bp with a GC content of 29.6% and 205 ORFs for vB_SsapH-Golestan101-M, and 142,199 bp with a GC content of 30.6% and 203 ORFs for vB_SsapH-Golestan-105-M. A bioinformatics analysis indicated that all three phages belong to the Twortvirinae subfamily of Herelleviridae. Among the three phages, vB_SsapH-Golestan-100 exhibited the least similarity to previously known phages, with less than 21% similarity with its closest counterparts in genomic databases.

CONCLUSIONS

This study identified new phages that have the ability to destroy a broad range of S. saprophyticus isolates and may potentially be classified as a new genus and species within the Herelleviridae family in future studies.

Exploration of Novel Antimicrobial Agents against Foodborne Pathogens via a Deep Learning Approach

The emergence of antibiotic-resistant bacteria poses a severe threat to food safety and human health, necessitating an urgent search for novel antimicrobial agents that can be applied in the food industry. This study utilizes a deep learning approach to establish the optimal models for antibacterial activity against foodborne pathogens, particularly Escherichia coli and Staphylococcus aureus, as well as for predicting carcinogenicity. These optimal models are applied to screen natural products from the COCONUT database, resulting in the identification of 130 compounds with both antibacterial activity and noncarcinogenic properties. Two natural products, bis(hexamethylene)triamine and N-phenethylbiguanide, are selected for experimental validation of their antibacterial activity. The confirmation of antimicrobial properties validates the reliability of the models developed in this study. By providing an innovative approach for identifying antimicrobial agents for foodborne pathogens, this research offers new insights for discovering effective antimicrobials in an efficient manner.

The LAMP-CRISPR-Cas13a technique for detecting the CBASS mechanism of phage resistance in bacteria

Introduction

Antimicrobial resistance (AMR) is a major public health threat, driving the need for alternative treatments such as phage therapy. However, bacterial defense mechanisms, often regulated by the quorum sensing (QS) network and encoded in genomic islands (GIs), can generate phage-resistant mutants. Understanding these resistance mechanisms is essential for optimizing phage therapy.

Methods

This study analyzed 48 Klebsiella pneumoniae strains to identify pathogenicity islands (PAIs) containing anti-phage defense (APD) proteins. We constructed a knockout strain lacking the cyclase gene from the type II CBASS defense systems present in PAIs to investigate QS regulation and its role in cell viability. The LAMP-CRISPR-Cas13a technique was used to confirm gene knockout and to detect the main cyclase in type I CBASS systems, i.e., APECO1.

Results

A total of 309 pathogenicity islands (PAIs), containing 22.1% of anti-phage defense (APD) proteins, were identified. Type I and II CBASS APD systems were also detected in the genome of the 48, K. pneumoniae strains, and only two type II CBASS systems were located in PAIs. Alluding to these defense mechanisms, the QS revealed to be involved in the regulation of the type II CBASS systems contained in PAIs. Finally, the LAMP-CRISPR-Cas13a technology successfully detected the main cyclases habored in type I and II CBASS systems, respectively.

Discussion

The study findings highlight the regulatory role of the QS network in APD systems. Notably, this is the first study to develop an innovative biotechnological application for the LAMP-CRISPR-Cas13a rapid-technique (<2 h), thereby helping to optimize phage therapy by detecting bacterial resistance mechanisms and predicting the potential inefficacy of therapeutic phages and thus improving patient prognosis.

Genomic and proteomic characterization of four novel Schitoviridae family phages targeting uropathogenic Escherichia coli strain

BACKGROUND

Escherichia coli-associated urinary tract infections (UTIs) are among the most prevalent bacterial infections in humans. Typically, antibiotic medication is used to treat UTIs, but over the time, growth of multidrug resistance among these bacteria has created a global public health issue that necessitates other treatment modalities, such as phage therapy.

METHODS

The UPEC strain PSU-5266 (UE-17) was isolated from human urine samples, while phages were obtained from wastewater. These phages were characterized through host range analysis, stability studies, adsorption assays, and electron microscopy. Additionally, genomic, phylogenetic, and proteomic analyses were conducted to provide further insights.

RESULTS

The current study describes the isolation and characterization of four Escherichia coli phages designated as UE-S5a, UE-S5b, UE-M3 and UE-M6. Bactericidal assays depicted that all bacteriophages exhibited a strong lytic ability against uropathogenic E. coli (UPEC) strain PSU-5266 (UE-17). The phages displayed a broad host range (31-41%) among 104 tested isolates and adsorption rate of 15-20 min. They were stable within pH range of 5-11 and temperature range of 4 to 55 °C. Electron microscopy showed that all phages have icosahedral heads (70-74 nm) and short non-contractile tails, thus exhibiting a podovirus morphology. Sequencing results showed that they have linear double stranded DNA, genome of 73 to 76 kb in length, with GC content of 42% and short direct terminal repeats. Their genomes contain 84-88 predicted genes with putative functions predicted to 42-48% of gene products. The phylogenetic and comparative genomic analysis results depicted that these phages, sharing > 98% sequence similarity, are new members of genus Gamaleyavirus of subfamily Enquatrovirinae, in the Schitoviridae family. Mass spectrometric analysis of purified phage particles identified 44-56 phage particle-associated proteins (PPAPs) belonging to various functional groups such as lysis proteins, structural proteins, DNA packaging related proteins, and proteins involved in replication, metabolism and regulation. In addition, no genes encoding virulence factors, antibiotic resistance or lysogeny factors were identified.

CONCLUSION

The overall findings suggest that these bacteriophages are potential candidates for phage therapy in treating UTIs caused by UPEC strains.

From Dormancy to Eradication: Strategies for Controlling Bacterial Persisters in Food Settings

Bacterial persistence, a dormant state that enables microorganisms to survive harsh conditions, is a significant concern in food-industry settings, where traditional antimicrobial treatments often fail to eliminate these resilient cells. This article goes beyond conventional review by compiling critical information aimed at providing practical solutions to combat bacterial persisters in food production environments. This review explores the primary mechanisms behind persister cell formation, including toxin-antitoxin systems, the alarmone guanosine tetraphosphate (ppGpp), stochastic processes (in which persistence occurs as a random event), and the SOS response. Given the serious implications for food safety and quality, the authors also report a range of physical, chemical, and biological methods for targeting and eradicating persister cells. The strategies discussed, whether applied individually or in combination, offer varying levels of availability and applicability within the industry and can serve as a guide for implementing microbial contamination control plans. While significant progress has been achieved, further research is crucial to fully understand the complex mechanisms underlying bacterial persistence in food and to develop effective and targeted strategies for its eradication in food-industry settings. Overall, the translation of these insights into practical applications aims to support the food industry in overcoming this persistent challenge, ensuring safer, more sustainable food production.

Beyond antibiotics: exploring multifaceted approaches to combat bacterial resistance in the modern era: a comprehensive review

Antibiotics represent one of the most significant medical breakthroughs of the twentieth century, playing a critical role in combating bacterial infections. However, the rapid emergence of antibiotic resistance has become a major global health crisis, significantly complicating treatment protocols. This paper provides a narrative review of the current state of antibiotic resistance, synthesizing findings from primary research and comprehensive review articles to examine the various mechanisms bacteria employ to counteract antibiotics. One of the primary sources of antibiotic resistance is the improper use of antibiotics in the livestock industry. The emergence of drug-resistant microorganisms from human activities and industrial livestock production has presented significant environmental and public health concerns. Today, resistant nosocomial infections occur following long-term hospitalization of patients, causing the death of many people, so there is an urgent need for alternative treatments. In response to this crisis, non-antibiotic therapeutic strategies have been proposed, including bacteriophages, probiotics, postbiotics, synbiotics, fecal microbiota transplantation (FMT), nanoparticles (NPs), antimicrobial peptides (AMPs), antibodies, traditional medicines, and the toxin-antitoxin (TA) system. While these approaches offer innovative solutions for addressing bacterial infections and preserving the efficacy of antimicrobial therapies, challenges such as safety, cost-effectiveness, regulatory hurdles, and large-scale implementation remain. This review examines the potential and limitations of these strategies, offering a balanced perspective on their role in managing bacterial infections and mitigating the broader impact of antibiotic resistance.

Genomic epidemiology and public health implications of zoonotic monophasic Salmonella Typhimurium ST34

Background

Monophasic Salmonella Typhimurium sequence type 34 (mSTM ST34) has emerged as a significant global health threat, but our understanding of its genomic epidemiology and potential public health implications in international and regional contexts remains limited. This study aims to fill this crucial gap by assessing the genomic epidemiology of multidrug resistance (MDR) mSTM ST34, as well as its clinical characteristics and virulence.

Methods

To achieve the objectives of this study, we conducted a comprehensive genomic analysis of mSTM ST34 isolates. We obtained a global dataset comprising 13,844 strains from public databases, along with 339 strains from a regional surveillance collection in Zhejiang Province, China. This dataset aims to provide in-depth insights into antimicrobial resistance, mobile genetic elements, and pathogenicity. Additionally, we meticulously assessed the association between phenotypic profiles and clinical presentations.

Results

Our findings revealed that the prevalence of mSTM ST34 has surpassed that of the previously dominant ST19. In addition, we observed an increase in the detection of the IncQ1 plasmid, which is responsible for disseminating MDR. The prevalence of mSTM ST34 carriage was exceptionally high among children (≤12 years old) and elderly individuals (≥65 years old), with 92.6% of the isolates exhibiting MDR, including resistance to frontline antimicrobials such as third-generation cephalosporins and ciprofloxacin. Additionally, the human mSTM ST34 strain demonstrates a remarkable capacity for biofilm formation, which increases its virulence in animal models and complicates therapeutic interventions.

Conclusions

mSTM ST34 has surpassed the previously dominant ST19, and its ability to transmit across multi-species increases its potential for further human transmission. This study addresses critical gaps in our understanding of mSTM ST34 prevalence, highlighting the importance of whole genome sequencing in surveilling zoonotic pathogens.

Environmental hygiene strategies to combat antimicrobial resistance in healthcare settings

In this manuscript, we highlight current literature on environmental hygiene techniques to combat reservoirs of antibiotic resistant organisms in the healthcare environment. We discuss several topics for each strategy, including mechanism of action, assessment of effectiveness based on studies, cost, and real-world translatability. The techniques and topics summarized here are not inclusive of all available environmental hygiene techniques but highlight some of the more popular and investigated strategies. We focus on the following: Ultraviolet radiation, hydrogen peroxide vapor, copper-coated surfaces, phages, interventions involving sinks, and educational initiatives.

Bacteriophage therapy for multidrug-resistant infections: current technologies and therapeutic approaches

Bacteriophage (phage) therapy has emerged as a promising solution to combat the growing crisis of multidrug-resistant (MDR) infections. There are several international centers actively engaged in implementation of phage therapy, and recent case series have reported encouraging success rates in patients receiving personalized, compassionate phage therapy for difficult-to-treat infections. Nonetheless, substantial hurdles remain in the way of more widespread adoption and more consistent success. This Review offers a comprehensive overview of current phage therapy technologies and therapeutic approaches. We first delineate the common steps in phage therapy development, from phage bank establishment to clinical administration, and examine the spectrum of therapeutic approaches, from personalized to fixed phage cocktails. Using the framework of a conventional drug development pipeline, we then identify critical knowledge gaps in areas such as cocktail design, formulation, pharmacology, and clinical trial design. We conclude that, while phage therapy holds promise, a structured drug development pipeline and sustained government support are crucial for widespread adoption of phage therapy for MDR infections.

The high efficiency protective effectiveness of a newly isolated myoviruses bacteriophage vB_AceP_PAc in protecting mice from Aeromonas caviae infection in mice

Phage therapy is an effective strategy to combat multidrug resistance in bacteria and has been increasingly utilized to protect animals from bacterial infections. This study involved the isolation and purification of a novel myoviruses phage, vB_AceP_PAc, from a drug-resistant bacterial strain Aeromonas caviae. Genome sequence analysis based on nucleotide sequences revealed that vB_AceP_PAc shared significant similarity with the genomes of 10 other Aeromonas phages, with the highest coverage rate of 52% with phiA047. Intraperitoneal injection of 1 × 10⁷ CFU/mL (100 µL/mouse) A. caviae AC-CY resulted in diarrhea in mice three days later. At this time, oral administration of 1 × 109 PFU/mL (100 µL/mouse) vB_AceP_PAc effectively alleviated the diarrhea induced by Pseudomonas aeruginosa infection in the mice. Furthermore, oral administration of 1 × 109 PFU/ml vB_AceP_PAc (100 µl/mouse) in healthy mice significantly reduced inflammatory cytokine levels, increased tight junction molecule levels, and improved intestinal barrier function. Moreover, the consumption of vB_AceP_PAc by health mice led to a significant increase in the abundance of Lactobacillaceae in the gut, while the expression of CD3+CD4+/CD3+CD8+ was minimally affected. Overall, the findings of this study confirmed the promising potential of bacteriophage vB_AceP_PAc in treating diarrhea caused by A. caviae.

Isolation, characterization and genomic analysis of bacteriophages for biocontrol of vibriosis caused by Vibrio alginolyticus

Vibrio alginolyticus is a significant opportunistic pathogen in marine environments, affecting both marine organisms and humans. The rise of antibiotic-resistant strains has prompted the exploration of bacteriophages as alternative biological control agents. In this study, 414 lytic bacteriophages specific to V. alginolyticus were isolated from various seafood and environmental samples. Phages P122, P125, and P160 demonstrated the broadest host range, effectively lysing 79.01 % of fish pathogenic V. alginolyticus strains and 44.69 % of environmental strains. However, no activity was observed against clinical V. alginolyticus strains or other tested species, including V. harveyi, Escherichia coli, Staphylococcus aureus, and Aeromonas hydrophila. One-step growth curve analysis revealed latent periods of 40 to 60 min and burst sizes ranging from 140 to 367 PFU/infected cells. Transmission electron microscopy (TEM) classified these phages within the class of Caudoviricetes with an icosahedral head and a long non-contractile tail. Moreover, whole-genome sequencing (WGS) identified genome sizes of approximately 76 kb, with 272-280 open reading frames (ORFs), no tRNA and pathogenic-associated genes. Comparative genomic analysis showed over 97 % similarity with other Vibrio phages. Phylogenetic analysis based on the terminase subunit also confirmed phages P122, P125, and P160 belonging to the class of Caudoviricetes. The phages were non-toxic to Galleria mellonella larvae and showed promise in reducing mortality rates when used as a cocktail treatment. The study highlights the potential of these phages as effective biocontrol agents in aquaculture, offering a promising alternative to antibiotics for managing Vibrio infections.

Balancing act: counteracting adverse drug effects on the microbiome

The human gut microbiome, a community of microbes that plays a crucial role in our wellbeing, is highly adaptable but also vulnerable to drug treatments. This vulnerability can have serious consequences for the host, for example, increasing susceptibility to infections, immune, metabolic, and cognitive disorders. However, the microbiome's adaptability also provides opportunities to prevent, protect, or even reverse drug-induced damage. Recently, several innovative approaches have emerged aimed at minimizing the collateral damage of drugs on the microbiome. Here, we outline these approaches, discuss their applicability in different treatment scenarios, highlight current challenges, and suggest avenues that may lead to an effective protection of the microbiome.

Phage therapeutic delivery methods and clinical trials for combating clinically relevant pathogens

The ongoing global health crisis caused by multidrug-resistant (MDR) bacteria necessitates quick interventions to introduce new management strategies for MDR-associated infections and antimicrobial agents' resistance. Phage therapy emerges as an antibiotic substitute for its high specificity, efficacy, and safety profiles in treating MDR-associated infections. Various in vitro and in vivo studies denoted their eminent bactericidal and anti-biofilm potential. This review addresses the latest developments in phage therapy regarding their attack strategies, formulations, and administration routes. It additionally discusses and elaborates on the status of phage therapy undergoing clinical trials, and the challenges encountered in their usage, and explores prospects in phage therapy research and application.

Novel antimicrobial strategies for diabetic foot infections: addressing challenges and resistance

AIMS

This review examines the challenges posed by Diabetic Foot Infections (DFIs), focusing on the impact of neuropathy, peripheral arterial disease, immunopathy, and the polymicrobial nature of these infections. The aim is to explore the factors contributing to antimicrobial resistance and assess the potential of novel antimicrobial treatments and drug delivery systems in improving patient outcomes.

METHOD

A comprehensive analysis of existing literature on DFIs was conducted, highlighting the multifactorial pathogenesis and polymicrobial composition of these infections. The review delves into the rise of antimicrobial resistance due to the overuse of antimicrobials, biofilm formation, and microbial genetic adaptability. Additionally, it considers glycemic control, patient adherence, and recurrence rates as contributing factors to treatment failure. Emerging therapies, including new antimicrobial classes and innovative drug delivery systems, were evaluated for their potential efficacy.

RESULTS

DFIs present unique treatment challenges, with high rates of antimicrobial resistance and poor response to standard therapies. Biofilm formation and the genetic adaptability of pathogens worsen resistance, complicating treatment. Current antimicrobial therapies are further hindered by poor glycemic control and patient adherence, leading to recurrent infections. Novel antimicrobial classes and innovative delivery systems show promise in addressing these challenges by offering more targeted, effective treatments. These new approaches aim to reduce resistance and improve treatment outcomes.

CONCLUSION

DFIs remain a clinical challenge due to their multifactorial nature and antimicrobial resistance. The development of novel antimicrobials and drug delivery systems is crucial to improving patient outcomes and combating resistance. Future research should focus on enhancing treatment efficacy, reducing resistance, and addressing patient adherence to reduce the burden of DFIs.

Microbial Technologies Enhanced by Artificial Intelligence for Healthcare Applications

The combination of artificial intelligence (AI) with microbial technology marks the start of a major transformation, improving applications throughout biotechnology, especially in healthcare. With the capability of AI to process vast amounts of biological big data, advanced microbial technology allows for a comprehensive understanding of complex biological systems, advancing disease diagnosis, treatment and the development of microbial therapeutics. This mini review explores the impact of AI-integrated microbial technologies in healthcare, highlighting advancements in microbial biomarker-based diagnosis, the development of microbial therapeutics and the microbial production of therapeutic compounds. This exploration promises significant improvements in the design and implementation of health-related solutions, steering a new era in biotechnological applications.

Phage treatment of multidrug-resistant bacterial infections in humans, animals, and plants: The current status and future prospects

Phages, including the viruses that lyse bacterial pathogens, offer unique therapeutic advantages, including their capacity to lyse antibiotic-resistant bacteria and disrupt biofilms without harming the host microbiota. The lack of new effective antibiotics and the growing limitations of existing antibiotics have refocused attention on phage therapy as an option in complex clinical cases such as burn wounds, cystic fibrosis, and pneumonia. This review describes clinical cases and preclinical studies in which phage therapy has been effective in both human and veterinary medicine, and in an agricultural context. In addition, critical challenges, such as the narrow host range of bacteriophages, the possibility of bacterial resistance, and regulatory constraints on the widespread use of phage therapy, are addressed. Future directions include optimizing phage therapy through strategies ranging from phage cocktails to broadening phage host range through genetic modification, and using phages as vaccines or biocontrol agents. In the future, if phage can be efficiently delivered, maintained in a stable state, and phage-antibiotic synergy can be achieved, phage therapy will offer much needed treatment options. However, the successful implementation of phage therapy within the current standards of practice will also require the considerable development of regulatory infrastructure and greater public acceptance. In closing, this review highlights the promise of phage therapy as a critical backup or substitute for antibiotics. It proposes a new role as a significant adjunct to, or even replacement for, antibiotics in treating multidrug-resistant bacterial infections.

The Role of Quorum Sensing in Phage Lifecycle Decision: A Switch Between Lytic and Lysogenic Pathways

Phages, the most abundant and diverse lifeforms on Earth, require strict parasitism for survival. During infection, temperate phages integrate both intracellular and extracellular host information to decide between lysis and lysogeny for replication. While various environmental and physiological factors influence the lysis-lysogeny decision, recent insights into phage-bacterium interactions reveal phages' ability to communicate with and influence bacteria, leveraging the host's quorum sensing system or small molecular signals. This article provides a succinct overview of current research advancements in this field, enhancing our understanding of phage-host dynamics and providing insights into bacteria's multicellular behavior in antiviral defense.

Anti-Infective Bacteriophage Immobilized Nitric Oxide-Releasing Surface for Prevention of Thrombosis and Device-Associated Infections

The treatment of critically ill patients has made great strides in the past few decades due to the rapid development of indwelling medical devices. Despite immense advancements in the design of these devices, indwelling medical device-associated infections and thrombosis are two major clinical problems that may lead to device failure and compromise clinical outcomes. Antibiotics are the current treatment choice for these infections; however, the global emergence of antibiotic-resistance and their biofilm formation abilities complicate the management of such infections. Moreover, systemic administration of anticoagulants has been used to counter medical device-induced thrombosis, but a range of serious adverse effects associated with all types of available anticoagulants entails exploring alternative options to counter device-associated thrombosis. In this study, bacteriophages (phages) were covalently immobilized on polydimethylsiloxane (PDMS) surface containing the nitric oxide (NO) donor S-nitroso-N-acetylpenicillamine (SNAP) via SNAP impregnation method. This dual strategy combines the targeted antibacterial activity of phages against bacterial pathogens with the antibacterial-antithrombotic activity of NO released from the polymeric surface. The PDMS, SNAP-PDMS, phage-immobilized PDMS (PDMS-Phage), and phage-immobilized SNAP-PDMS (SNAP-PDMS-Phage) surfaces were characterized for their surface topology, elemental composition, contact angle, SNAP loading, NO release and phage distribution. SNAP-PDMS and SNAP-PDMS-Phage surfaces showed similar and consistent NO release profiles over 24 h of incubation. Immobilization of whole phages on PDMS and SNAP-PDMS was achieved with densities of 2.4 ± 0.54 and 2.1 ± 0.33 phages μm-2, respectively. Immobilized phages were found to retain their activity, and SNAP-PDMS-Phage surfaces showed a significant reduction in planktonic (99.99 ± 0.08%) as well as adhered (99.80 ± 0.05%) Escherichia coli as compared to controls in log killing assays. The SNAP-PDMS-Phage surfaces also exhibited significantly reduced platelet adhesion by 64.65 ± 2.95% as compared to control PDMS surfaces. All fabricated surfaces were found to be nonhemolytic and do not exhibit any significant cytotoxic effects toward mammalian fibroblast cells. This study is the first of its kind to demonstrate the combinatorial pertinence of phages and NO to prevent antibiotic-resistant/sensitive bacterial infections and thrombosis associated with indwelling medical devices.

Phages as potential life-saving therapeutic option in the treatment of multidrug-resistant urinary tract infections

Urinary tract infections (UTIs) are among the most common bacterial infections worldwide and increasing antimicrobial resistance (AMR) challenges conventional antibiotic treatments. Phage therapy (PT) has emerged as a promising alternative due to its specificity, safety and efficacy against multidrug-resistant (MDR) pathogens causing infectious diseases. PT demonstrates significant potential in treating chronic and recurrent UTIs, also including catheter-associated infection by reducing bacterial biofilms, delaying catheter blockage, and enhancing antibiotic efficacy when used in combination. Clinical trials and case studies have reported high rates of bacterial eradication and symptom improvement with minimal side effects. Although endotoxin release and immune activation during treatment should continue to be investigated. The aim of this review is to present issues related to the use of phages in the treatment of UTIs of various etiological origins in selected patients, including those with comorbidities, taking into account the legal regulations, safety and effectiveness of this experimental therapy. The growing prevalence of MDR uropathogens highlights the urgent need for alternative therapies, such as those based on phages in order to treat antibiotic-resistant infections and improve patient outcomes. Despite the great potential of PT, its clinical implementation and use of phages as a routine treatment for bacterial infections requires rigorous trials, standardized production protocols and regulatory advancements.

Impact of Antimicrobial Resistance of Pseudomonas aeruginosa in Urine of Small Companion Animals in Global Context: Comprehensive Analysis

The isolation of multidrug-resistant (MDR) bacteria from the urinary tracts of pets is increasingly common, particularly in animals with concurrent health conditions. Pseudomonas aeruginosa (PA) is one of the most significant antimicrobial-resistant bacteria affecting cats and dogs within the European Union (EU). This study aims to review the prevalence and antimicrobial resistance patterns of PA isolated from urine samples of small animals globally. This pathogen is known for its opportunistic infections and is a significant concern in veterinary medicine due to its inherent resistance to multiple antibiotics and its ability to acquire additional resistance mechanisms. This review seeks to enhance educational initiatives regarding the management of emerging MDR bacteria.

Combating enteropathogenic and multidrug resistant Escherichia coli using the lytic bacteriophage vB_EcoM_ECO78, which disrupts bacterial biofilm formation and exhibits a remarkable environmental stability

AIM

The current study aimed to establish a phenotypic and genotypic characterization record of a novel lytic bacteriophage (phage) against multidrug-resistant (MDR) Escherichia coli (E. coli) infections.

METHODS AND RESULTS

Phenotypic characterization of the isolated phage included the assessment of phage morphology, host range, stability, and antibiofilm activity. The isolated phage vB_EcoM_ECO78 demonstrated a high lytic activity against MDR E. coli and E. coli serotypes O78: K80: H12 and O26: H11. Additionally, it showed a marked antibiofilm activity and high physical stability at a wide range of temperatures and pH. Genotypic investigations identified a double-stranded DNA genome of 165 912 base pairs (bp) spanning 258 open reading frames (ORFs), out of which 149 ORFs were identified and annotated. In vivo analysis further confirmed the therapeutic potential of vB_EcoM_ECO78 which effectively increased the survival of mice infected with MDR E. coli.

CONCLUSION

The isolated phage vB_EcoM_ECO78 exhibits considerable stability and antibiofilm activity against MDR E. coli isolates, supported by notable environmental fitness and in vivo antibacterial capability.

Failure or future? Exploring alternative antibacterials: a comparative analysis of antibiotics and naturally derived biopolymers

The global crisis of antimicrobial resistance (AMR) is escalating due to the misuse and overuse of antibiotics, the slow development of new therapies, and the rise of multidrug-resistant (MDR) infections. Traditional antibiotic treatments face limitations, including the development of resistance, disruption of the microbiota, adverse side effects, and environmental impact, emphasizing the urgent need for innovative alternative antibacterial strategies. This review critically examines naturally derived biopolymers with intrinsic (essential feature) antibacterial properties as a sustainable, next-generation alternative to traditional antibiotics. These biopolymers may address bacterial resistance uniquely by disrupting bacterial membranes rather than cellular functions, potentially reducing microbiota interference. Through a comparative analysis of the mechanisms and applications of antibiotics and antibacterial naturally derived biopolymers, this review highlights the potential of such biopolymers to address AMR while supporting human and environmental health.

Isolation and characterization of a broad-spectrum bacteriophage against multi-drug resistant Escherichia coli from waterfowl field

Escherichia coli (E. coli) is a significant pathogen responsible for intestinal infections and foodborne diseases. The rise of antibiotic resistance poses a significant challenge to global public health. Traditional antibiotic therapy is becoming increasingly ineffective, highlighting the urgent need for innovative control strategies. This study explores the potential of bacteriophages as a sustainable alternative to traditional antibiotics. From 2021 to 2022, a total of 183 non-repetitive duck source fecal samples were collected from Mianyang City, Sichuan Province, and 126 strains of E. coli were isolated. The minimum inhibitory concentration (MIC) test showed that these strains exhibited high resistance to piperacillin (96.8%), tetracycline (88.9%), and chloramphenicol (86.5%). It is concerning that 93.7% of the isolates are classified as multidrug-resistant (MDR), posing a significant threat to existing treatment options. 20 bacteriophages were isolated from fecal and soil samples, among which 5 bacteriophages were selected for further analysis. Bacteriophage YP6 showed excellent lytic effects on MDR strains, especially strain MY104, as well as representative serotypes O1 (E. coli MY51) and O18 (E. coli MY106). The identification of YP6 as a member of the Myoviridae family was conducted using transmission electron microscopy, and it was found to have an optimal infection factor of 0.1. Bacteriophages exhibit significant thermal and pH stability, maintaining survival at temperatures up to 60 °C and pH ranges of 4 to 10. Whole genome sequencing confirmed that YP6 has a double stranded DNA genome of 139,323 base pairs (bp), and no antibiotic resistance or virulence genes were found, indicating a low possibility of horizontal gene transfer. In addition, YP6 effectively inhibits the formation of E. coli biofilm, which is a key factor in chronic infections. The in vivo experiments using Galleria mellonella (G. mellonella) larvae have shown that it has a significant protective effect against MDR E. coli infection. In summary, bacteriophage YP6 is expected to become a therapeutic agent against MDR E. coli infection due to its broad host range, environmental stability, and biofilm inhibition properties. Future research should optimize bacteriophage preparations, evaluate the safety and efficacy of animal models, and establish clinical application plans in the field of food safety.

Bacteriophage Treatment Induces Phenotype Switching and Alters Antibiotic Resistance of ESBL Escherichia coli

Background/Objectives: Bacteriophage therapy represents a promising strategy to combat multidrug-resistant pathogens, such as Escherichia coli. In this study, we explored the effects of a bacteriophage infection on an Extended Spectrum Beta-Lactamase (ESBL) positive E. coli isolate. Methods: We used next generation sequencing, proteomics and phenotypic screens to investigate the effect of bacteriophage infections on E. coli metabolism and resistance phenotypes. Results: The bacteriophage infection led to notable alterations in colony morphology, indicating profound changes in bacterial metabolism. Proteomic analysis revealed significant shifts in protein expression, with 65 proteins upregulated and 246 downregulated post-infection. The downregulated proteins were involved in various metabolic pathways, including nucleic acid, protein and lipid metabolism, and iron acquisition. Bacteriophage treatment also led to increased bacterial membrane permeability. Altogether, these alterations in bacterial metabolism and membrane permeability may lead to a general reduction in antibiotic resistance. Indeed, the bacteriophage-infected E. coli exhibited increased sensitivity to various classes of antibiotics, including beta-lactams, fluoroquinolones, trimethoprim-sulfamethoxazole, and aminoglycosides. Conclusions: Our findings highlight the potential of bacteriophage therapy as an adjunct to existing antibiotics, enhancing their efficacy against resistant strains.

Chitosan nano-formulation enhances stability and bactericidal activity of the lytic phage HK6

BACKGROUND

Successful treatment of pathogenic bacteria like Enterobacter Cloacae with bacteriophage (phage) counteract some hindrance such as phage stability and immunological clearance. Our research is focused on the encapsulation of phage HK6 within chitosan nanoparticles.

RESULT

Encapsulation significantly improves stability, efficacy, and delivery of phages. Chitosan nanoparticles (CS-NPs) achieve a phage entrapment efficiency of 97%. Fourier-transform infrared spectroscopy (FT-IR) reveals shifts towards higher wavenumbers and a new peak, indicating amide bond formation and successful phage encapsulation. The average particle sizes for CS-NP and phage HK6 encapsulated CS-NPs were 180 ± 10 nm and 297 ± 18 nm, respectively. Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) analyses reveal that phage HK6 encapsulated CS-NPs are larger on average than CS-NPs, highlighting successful phage encapsulation. Encapsulated bacteriophages maintain its effectiveness at higher pH levels of 11 and 12. Both encapsulated and free bacteriophages are thermostable between 25 and 60 °C; while at higher temperatures (up to 80 °C), the encapsulated phage is thermally stable. Over four days, 70.57% of phages were released from encapsulated CS-NPs. Encapsulation of bacteriophage HK6 in CS-NPs enhances antibacterial activity within the first 2 h, compared to phage or nanoparticles alone.

CONCLUSION

This suggests that the phage HK6 encapsulated CS-NPs exhibit potentiality as biocontrol agents against resistant microorganisms offering an alternative to phage alone.

Gut Microbiota Secondary Metabolites: Key Roles in GI Tract Cancers and Infectious Diseases

The gut microbiota, a dynamic ecosystem of trillions of microorganisms, produces secondary metabolites that profoundly influence host health. Recent research has highlighted the significant role of these metabolites, particularly short-chain fatty acids, indoles, and bile acids, in modulating immune responses, impacting epigenetic mechanisms, and contributing to disease processes. In gastrointestinal (GI) cancers such as colorectal, liver, and gastric cancer, microbial metabolites can drive tumorigenesis by promoting inflammation, DNA damage, and immune evasion. Conversely, these same metabolites hold therapeutic promise, potentially enhancing responses to chemotherapy and immunotherapy and even directly suppressing tumor growth. In addition, gut microbial metabolites play crucial roles in infectious disease susceptibility and resilience, mediating immune pathways that impact pathogen resistance. By consolidating recent insights into the gut microbiota's role in shaping disease and health, this review underscores the therapeutic potential of targeting microbiome-derived metabolites for treating GI cancers and infectious diseases and calls for further research into microbiome-based interventions.

An insight into the applications of bacteriophages against food-borne pathogens

Novel and emerging pathogens, enduring contamination, antibiotic resistance, an environment that is always changing, and the complexity of food production systems all contribute to the worsening of foodborne illness. It has been proposed that bacteriophages can serve as both fast food-borne pathogen detection tools and natural food preservatives in a variety of foods. Phages, like many other antimicrobial interventions used in food production systems, are not a cure-all for issues related to food safety, though. Consequently, phage-based biocontrol has a generally narrower antibacterial spectrum than most antibiotics, even though it can be promising in the fight against foodborne infections. Among the difficulties phage-based biocontrol techniques encounter are forming phage-insensitive single-cell variations and creating potent cocktails. To better understand when and where phage-based applications can be successfully implemented at the production and processing levels, this review focuses on phage-based applications at crucial control points in food production systems.

Insights from Shigella bacteriophage genomes analysis

Shigella species, a major cause of shigellosis, remain a substantial global health issue and the emergence of antibiotic-resistant Shigella strains has aggravated the situation. Hence, four Shigella phages were investigated to provide insights into the evolutionary trajectories and genomic properties of Shigella-infecting bacteriophages using comparative genome analysis. Analysis shows that these four phages belong to the Tequatrovirus genus and include a considerable number of proteins for 'Tail' and "DNA, RNA and Nucleotide Metabolism," indicating their aptitude for specialized host interaction and replication efficiency. The identification of 10 tRNAs further support that, these phages have high replication efficiency. Thus, this study improves our understanding of phage evolution by exposing the genetic mechanisms that drive phage adaptability and host specificity. This also highlights the significance of phage genomic research in developing viable therapies for antibiotic-resistant Shigella infections.

Optimization of bacteriophage propagation in high-yield continuous culture (cellstat) meeting the constraints of industrial manufacturing processes

The growing use of bacteriophages in the fields of agriculture, agri-food, veterinary treatments, and medicine involves the quantitative production of these bacteriophages. In this study, we propose a bacteriophage production protocol that can easily be transposed to industry. We used a cellstat production system because the latest studies have shown that it is the most suitable process for the production of phages due to volumetric productivity, safety (limitation of co-evolution), and flexibility (choice of growth rate criteria). Sizing of the assembly used makes it possible to extrapolate the results to industrial production. The production conditions are indicated precisely, which would allow manufacturers to adapt the protocol to their own equipment. We propose experimental conditions in order to obtain a stable Escherichia coli population, qualitatively and over time, and production of high-titer T7 bacteriophages. The optimized production conditions (yield, cost and simplicity of the process) are: a buffered peptone water medium concentration of 11 g L-1 and a dilution rate of 1.6 h-1. Under these conditions, we obtained a production of 7.35×1016 plaque-forming units (PFU) L-1 day-1 with a concentration of 9.8×1012 PFU mL-1. The strength of this work lies in its focus on industrial applicability.

From forgotten cure to modern medicine: The resurgence of bacteriophage therapy

OBJECTIVES

The unregulated use of antibiotics has led to the rise of antibiotic-resistant bacterial strains. This study explores bacteriophage therapy as an alternative treatment, highlighting its history, significance, and advancements in Europe, the United States, and the Middle East.

METHODS

A comprehensive literature review on bacteriophage therapy was conducted, focusing on its development, clinical trials, and patient treatment applications. The study also examined challenges, limitations, criteria for ideal phage selection, and manipulation techniques.

RESULTS

The United States and several European countries have advanced in phage therapy, progressing from clinical trials to patient treatment, whereas Middle Eastern countries are still in the early stages. Bacteriophages offer specificity, abundance, and minimal side effects, but challenges like safety concerns and potential resistance limit their widespread use.

CONCLUSION

Bacteriophage therapy shows promise as an antibiotic alternative but faces safety and resistance challenges. Continued research and better regulatory frameworks, especially in the Middle East, are needed to realize its potential.

Isolation, Characterization, and Unlocking the Potential of Mimir124 Phage for Personalized Treatment of Difficult, Multidrug-Resistant Uropathogenic E. coli Strain

Escherichia coli and its bacteriophages are among the most studied model microorganisms. Bacteriophages for various E. coli strains can typically be easily isolated from environmental sources, and many of these viruses can be harnessed to combat E. coli infections in humans and animals. However, some relatively rare E. coli strains pose significant challenges in finding suitable phages. The uropathogenic strain E. coli UPEC124, isolated from a patient suffering from neurogenic bladder dysfunction, was found to be resistant to all coliphages in our collections, and initial attempts to isolate new phages failed. Using an improved procedure for phage enrichment, we isolated the N4-related phage Mimir124, belonging to the Gamaleyavirus genus, which was able to lyse this "difficult" E. coli strain. Although Mimir124 is a narrow-spectrum phage, it was effective in the individualized treatment of the patient, leading to pathogen eradication. The primary receptor of Mimir124 was the O antigen of the O101 type; consequently, Mimir124-resistant clones were rough (having lost the O antigen). These clones, however, gained sensitivity to some phages that recognize outer membrane proteins as receptors. Despite the presence of nine potential antiviral systems in the genome of the UPEC124 strain, the difficulty in finding effective phages was largely due to the efficient, non-specific cell surface protection provided by the O antigen. These results highlight the importance of an individualized approach to phage therapy, where narrow host-range phages-typically avoided in pre-fabricated phage cocktails-may be instrumental. Furthermore, this study illustrates how integrating genomic, structural, and functional insights can guide the development of innovative therapeutic strategies, paving the way for broader applications of phage therapy in combating multidrug-resistant bacterial pathogens.

Bacteriophage Therapy as a Promising Alternative for Antibiotic-Resistant Enterococcus faecium: Advances and Challenges

Enterococcus faecium is a Gram-positive bacterium increasingly identified as a critical nosocomial pathogen that poses significant treatment challenges due to its resistance to multiple antibiotics, particularly vancomycin-resistant E. faecium (VRE) strains. The urgent need for alternative therapeutic strategies has renewed interest in bacteriophage (phage) therapy, given phages specificity and bactericidal potential. This review explores the advancements in phage therapy against antibiotic-resistant E. faecium, including phage morphological diversity, genomic characteristics, and infection mechanisms. The efficacy of phage therapy in in vitro, ex vivo, and in vivo models and the compassionate use in clinical settings are evaluated, highlighting the promising outcomes of phage-antibiotic synergies and biofilm disruption. Key challenges and future research directions are discussed, with a focus on improving therapeutic efficacy and overcoming bacterial resistance. This review emphasizes the potential of phage therapy as a viable solution for managing multidrug-resistant E. faecium infections and underscores the importance of future investigations to enhance clinical applications.

Phage cocktail amikacin combination as a potential therapy for bacteremia associated with carbapenemase producing colistin resistant Klebsiella pneumoniae

The increasing occurrence of hospital-associated infections, particularly bacteremia, caused by extensively drug-resistant (XDR) carbapenemase-producing colistin-resistant Klebsiella pneumoniae highlights a critical requirement to discover new therapeutic alternatives. Bacteriophages having host-specific bacteriolytic effects are promising alternatives for combating these pathogens. Among 12 phages isolated from public wastewater in Thailand, two phages-vB_kpnM_05 (myovirus) and vB_kpnP_08 (podovirus) showed broad-host range, producing bacteriolytic activities against 81.3% (n = 26) and 78.1% (n = 25) of 32 XDR carbapenemase-producing colistin-resistant K. pneumoniae, with capsular types-K15, K17, K50, K51, K52/wzi-50 and K2/wzi-2. Both phages showed short replication times, large burst sizes with rapid adsorptions. They exhibited significant stability under various environmental conditions. Genomic analysis revealed that both phages are genetically distinct phages from Myoviridae and Podoviridae family, with the lack of toxin, virulence, lysogeny and antibiotic resistance genes. These characteristics highlighted their promising potential for utilizing in phage therapy for combating XDR K. pneumoniae. Although phage cocktail combining vB_kpnM_05 and vB_kpnP_08 provided significant bacteriolysis for longer duration (8 h) than its monophage (6 h), bacterial regrowth was observed which suggested an evitable development of phage resistance under phages' selection pressures. Future study will be undertaken to elucidate the precise mechanisms by which these XDR K. pneumoniae developed phage resistance and their associated fitness cost. Remarkably, combining phage cocktail with amikacin at their sub-inhibitory concentrations produced potent synergy by completely suppressing bacterial regrowth in vitro. Our study demonstrated the significant therapeutic and prophylactic effectiveness of a phage cocktail-amikacin combination as a promising alternative strategy for overcoming bacteremia associated with XDR K. pneumoniae having carbapenemase and colistin resistance in vivo.

Assessment of Bacteriophage Pharmacokinetic Parameters After Intra-Articular Delivery in a Rat Prosthetic Joint Infection Model

Prosthetic joint infections (PJIs) are a serious complication of orthopedic surgery. Bacteriophage (phage) therapy shows promise as an adjunctive treatment but requires further study, particularly in its pharmacokinetics. Consequently, we performed a pharmacokinetic assessment of phage therapy for PJIs using a Staphylococcus epidermidis Kirschner wire-based prosthesis rat model. We used 52 male Sprague-Dawley rats in four groups: negative controls (no phage, sterile implant), PJI controls (bacteria, no phage), sterile phage (phages given, sterile implant), and PJI (bacteria, phages given). The PJI groups were inoculated with ~106 CFU of S. epidermidis. The groups receiving phage were intra-articularly injected with ~108 PFU of vB_SepM_Alex five days post-implantation. The rats were euthanized between 30 min and 48 h post-injection. The measured phage concentrations between the PJI rats and the sterile controls in periarticular tissues were not significantly different. In a noncompartmental pharmacokinetic analysis, the estimated phage half-lives were under 6 h (combined: 3.73 [IQR, 1.45, 10.07]). The maximum phage concentrations were reached within 2 h after administration (combined: 0.75 [0.50, 1.75]). The estimated phage mean residence time was approximately three hours (combined: 3.04 [1.44, 4.19]). Our study provides a preliminary set of pharmacokinetic parameters that can inform future phage dosing studies and animal models of phage therapy for PJIs.

Designing a simple and efficient phage biocontainment system using the amber suppressor initiator tRNA

Multidrug-resistant infections are becoming increasingly prevalent worldwide. One of the fastest-emerging alternative and adjuvant therapies being proposed is phage therapy. Naturally isolated phages are used in the vast majority of phage therapy treatments today. Engineered phages are being developed to enhance the effectiveness of phage therapy, but concerns over their potential escape remain a salient issue. To address this problem, we designed a biocontained phage system based on conditional replication using amber stop codon suppression. This system can be easily installed on any natural phage with a known genome sequence. To test the system, we individually mutated the start codons of three essential capsid genes in phage φX174 to the amber stop codon (UAG). These phages were able to efficiently infect host cells expressing the amber initiator tRNA, which suppresses the amber stop codon and initiates translation at TAG stop codons. The amber phage mutants were also able to successfully infect host cells and reduce their population on solid agar and liquid culture but could not produce infectious particles in the absence of the amber initiator tRNA or complementing capsid gene. We did not detect any growth-inhibiting effects on E. coli strains known to lack a receptor for φX174 and we showed that engineered phages have a limited propensity for reversion. The approach outlined here may be useful to control engineered phage replication in both the lab and clinic.

Acidic polymers reversibly deactivate phages due to pH changes

Bacteriophages are promising as therapeutics and biotechnological tools, but they also present a problem for routine and commercial bacterial cultures, where contamination must be avoided. Poly(carboxylic acids) have been reported to inhibit phages' ability to infect their bacterial hosts and hence offer an exciting route to discover additives to prevent infection. Their mechanism and limitations have not been explored. Here, we report the role of pH in inactivating phages to determine if the polymers are unique or simply acidic. It is shown that lower pH (=3) triggered by either acidic polymers or similar changes in pH using HCl lead to inhibition. There is no inhibitory activity at higher pHs (in growth media). This was shown across a panel of phages and different molecular weights of commercial and controlled-radical polymerization-derived poly(acrylic acid)s. It is shown that poly(acrylic acid) leads to reversible deactivation of phage, but when the pH is adjusted using HCl alone the phage is irreversibly deactivated. Further experiments using metal binders ruled out ion depletion as the mode of action. These results show that polymeric phage inhibitors may work by unique mechanisms of action and that pH alone cannot explain the observed effects whilst also placing constraints on the practical utility of poly(acrylic acid).

Meeting report of the seventh annual Tri-Service Microbiome Consortium Symposium

The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among DoD organizations and to facilitate resource, material and information sharing among consortium members, which includes collaborators in academia and industry. The 2023 annual symposium was a hybrid meeting held in Washington DC on 26-27 September 2023 concurrent with the virtual attendance, with oral and poster presentations and discussions centered on microbiome-related topics within five broad thematic areas: 1) Environmental Microbiome Characterization; 2) Microbiome Analysis; 3) Human Microbiome Characterization; 4) Microbiome Engineering; and 5) In Vitro and In Vivo Microbiome Models. Collectively, the symposium provided an update on the scope of current DoD and DoD-affiliated microbiome research efforts and fostered collaborative opportunities. This report summarizes the presentations and outcomes of the 7th annual TSMC symposium.