Application of phage therapy: Synergistic effect of phage EcSw (ΦEcSw) and antibiotic combination towards antibiotic-resistant Escherichia coli

Phage-Modified Clear Hydrogel for Simultaneous Detection of Multiple Bacteria

The proliferation speed of live foodborne pathogens is fast. A small number of pathogens will have a great impact on food and the environment if positive samples are not detected timely. In this study, transparent porous hydrogel stir bars, modified by two different phages (corresponding to two different bacteria (Escherichia coli and Hafnia sp)), have been developed for rapid detection of foodborne bacteria. A large number of samples can be analyzed simultaneously with a small animal live imager device to screen out the positive samples, while an adenosine triphosphate (ATP) bioluminescence sensor can be used to quantify the number of bacteria in the positive samples. The phage has good specificity and capture ability to bacteria, which makes the method highly sensitive. In addition, the use of multiple phages also enables the method to detect multiple bacteria simultaneously. The three-dimensional structure of the hydrogel allows it to modify more phages, and its transparent nature also allows the inside bioluminescence to be detected. Both can enhance the sensitivity of the detection. Finally, the reagents needed for bioluminescence, such as d-luciferin, can also be preencapsulated in the hydrogel, thus simplifying the detection step. Under the best conditions, the detection range of the method is 102-108 CFU·mL-1, and the limit of detection is 30 CFU·mL-1 within 11 min. The test results of actual samples show that there is no difference between using the method developed through this study and the traditional plate counting method, but the detection time is greatly shortened.

Zebrafish as an effective model for evaluating phage therapy in bacterial infections: a promising strategy against human pathogens

The escalating prevalence of antibiotic-resistant bacterial infections necessitates urgent alternative therapeutic strategies. Phage therapy, which employs bacteriophages to specifically target pathogenic bacteria, emerges as a promising solution. This review examines the efficacy of phage therapy in zebrafish models, both embryos and adults, which are proven and reliable for simulating human infectious diseases. We synthesize findings from recent studies that utilized these models to assess phage treatments against various bacterial pathogens, including Enterococcus faecalis, Pseudomonas aeruginosa, Mycobacterium abscessus, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, and Escherichia coli. Methods of phage administration, such as circulation injection and bath immersion, are detailed alongside evaluations of survival rates and bacterial load reductions. Notably, combination therapies of phages with antibiotics show enhanced efficacy, as evidenced by improved survival rates and synergistic effects in reducing bacterial loads. We also discuss the transition from zebrafish embryos to adult models, emphasizing the increased complexity of immune responses. This review highlights the valuable contribution of the zebrafish model to advancing phage therapy research, particularly in the face of rising antibiotic resistance and the urgent need for alternative treatments.

Genome analysis of triple phages that curtails MDR E. coli with ML based host receptor prediction and its evaluation

Infections by multidrug resistant bacteria (MDR) are becoming increasingly difficult to treat and alternative approaches like phage therapy, which is unhindered by drug resistance, are urgently needed to tackle MDR bacterial infections. During phage therapy phage cocktails targeting different receptors are likely to be more effective than monophages. In the present study, phages targeting carbapenem resistant clinical isolate of E. coli U1007 was isolated from Ganges River (U1G), Cooum River (CR) and Hospital waste water (M). Capsid architecture discerned using TEM identified the phage families as Podoviridae for U1G, Myoviridae for CR and Siphoviridae for M phage. Genome sequencing showed the phage genomes varied in size U1G (73,275 bp) CR (45,236 bp) and M (45,294 bp). All three genomes lacked genes encoding tRNA sequence, antibiotic resistant or virulent genes. A machine learning (ML) based multi-class classification model using Random Forest, Logistic Regression, and Decision Tree were employed to predict the host receptor targeted by receptor binding protein of all 3 phages and the best performing algorithm Random Forest predicted LPS O antigen, LamB or OmpC for U1G; FhuA, OmpC for CR phage; and FhuA, LamB, TonB or OmpF for the M phage. OmpC was validated as receptor for U1G by physiological experiments. In vivo intramuscular infection study in zebrafish showed that cocktail of dual phages (U1G + M) along with colsitin resulted in a significant 3.5 log decline in cell counts. Our study highlights the potential of ML tool to predict host receptor and proves the utility of phage cocktail to restrict E. coli U1007 in vivo.

Antibacterial effects of single phage and phage cocktail against multidrug-resistant Klebsiella pneumoniae isolated from diabetic foot ulcer

Diabetic foot ulcer (DFU) is associated with long-term hospitalization and amputation. Antibiotic resistance has made the infection eradication more difficult. Hence, seeking alternative therapies such as phage therapy seems necessary. Bacteriophages are viruses targeting specific bacterial species. Klebsiella pneumoniae (K. pneumoniae) is among causative agents of the DFU. In this study, the therapeutic effects of single phage and phage cocktail were investigated against multidrug-resistant (MDR) K. pneumonia isolated from DFU. Bacteriophages were isolated from animal feces and sewage samples, and were enriched and propagated using K. pneumoniae as the host. Thirty K. pneumoniae clinical isolates were collected from hospitalized patients with DFU. The antibiotic susceptibility pattern was determined using agar disk diffusion test. The phages' morphological traits were determined using transmission electron microscopy (TEM). The killing effect of isolated phages was assessed using plaque assay. Four phage types were isolated and recognized including KP1, KP2, KP3, and KP4. The bacterial rapid regrowth was observed following each single phage-host interaction, but not phage cocktail due to the evolution of mutant strains. Phage cocktail demonstrated significantly higher antibacterial activity than each single phage (p < 0.05) without any bacterial regrowth. The employment of phage cocktail was promising for the eradication of MDR-K. pneumoniae isolates. The development of phage therapy in particular, phage cocktail is promising as an efficient approach to eradicate MDR-K. pneumoniae isolated from DFU. The application of a specific phage cocktail can be investigated to try and achieve the eradication of various infections.

Bacteriophage Therapy as an Application for Bacterial Infection in China

Antibiotic resistance has emerged as a significant issue to be resolved around the world. Bacteriophage (phage), in contrast to antibiotics, can only kill the target bacteria with no adverse effect on the normal bacterial flora. In this review, we described the biological characteristics of phage, and summarized the phage application in China, including in mammals, ovipara, aquatilia, and human clinical treatment. The data showed that phage had a good therapeutic effect on drug-resistant bacteria in veterinary fields, as well as in the clinical treatment of humans. However, we need to take more consideration of the narrow lysis spectrum, the immune response, the issues of storage, and the pharmacokinetics of phages. Due to the particularity of bacteriophage as a bacterial virus, there is no unified standard or regulation for the use of bacteriophage in the world at present, which hinders the application of bacteriophage as a substitute for antibiotic biological products. We aimed to highlight the rapidly advancing field of phage therapy as well as the challenges that China faces in reducing its reliance on antibiotics.

A newly isolated bacteriophage vB8388 and its synergistic effect with aminoglycosides against multi-drug resistant Klebsiella oxytoca strain FK-8388

The bacteriophage vB8388 can lyse multi-drug resistant Klebsiella oxytoca strain FK-8388 and maintain stability in a wide range of temperatures (from 4 °C to 80 °C) and pHs (3-11). Bioinformatics analysis showed that vB8388 is a linear double-stranded DNA virus that is 39,750 long with 50.65% G + C content and 44 putative open reading frames (ORFs). Phage vB8388 belongs to the family Autographviridae and possesses a non-contractile tail. The latency period of vB8388 was approximately 20 min. The combination of phage vB8388 and gentamicin, amikacin, or tobramycin could effectively inhibit the growth of K. oxytoca strain FK-8388, with a decrease of more than 4 log units within 12 h in vitro. Phage vB8388 showed a strong synergistic effect with gentamicin that could enhance the anti-biofilm effect of vB8388. The phage + gentamicin combination also showed synergy in vivo in the larval infection model of Galleria mellonella. In conclusion, the findings of this study suggest the potential of phage + antibiotic combination therapy to be used as an alternative therapeutic approach for treating infectious diseases caused by multidrug-resistant bacteria.

Alternatives Therapeutic Approaches to Conventional Antibiotics: Advantages, Limitations and Potential Application in Medicine

Resistance to antimicrobials and particularly multidrug resistance is one of the greatest challenges in the health system nowadays. The continual increase in the rates of antimicrobial resistance worldwide boosted by the ongoing COVID-19 pandemic poses a major public health threat. Different approaches have been employed to minimize the effect of resistance and control this threat, but the question still lingers as to their safety and efficiency. In this context, new anti-infectious approaches against multidrug resistance are being examined. Use of new antibiotics and their combination with new β-lactamase inhibitors, phage therapy, antimicrobial peptides, nanoparticles, and antisense antimicrobial therapeutics are considered as one such promising approach for overcoming bacterial resistance. In this review, we provide insights into these emerging alternative therapies that are currently being evaluated and which may be developed in the future to break the progression of antimicrobial resistance. We focus on their advantages and limitations and potential application in medicine. We further highlight the importance of the combination therapy approach, wherein two or more therapies are used in combination in order to more effectively combat infectious disease and increasing access to quality healthcare. These advances could give an alternate solution to overcome antimicrobial drug resistance. We eventually hope to provide useful information for clinicians who are seeking solutions to the problems caused by antimicrobial resistance.

Isolation and characterization of a novel Escherichia coli phage Kayfunavirus ZH4

Escherichia coli, a gram-negative bacterium, was generally considered conditional pathogenic bacteria and the proportion of bacteria resistant to commonly used specified antibacterial drugs exceeded 50%. Phage therapeutic application has been revitalized since antibiotic resistance in bacteria was increasing. Compared with antibiotics, phage is the virus specific to bacterial hosts. However, further understanding of phage-host interactions is required. In this study, a novel phage specific to a E. coli strain, named as phage Kayfunavirus ZH4, was isolated and characterized. Transmission electron microscopy showed that phage ZH4 belongs to the family Autographiviridae. The whole-genome analysis showed that the length of phage ZH4 genome was 39,496 bp with 49 coding domain sequence (CDS) and no tRNA was detected. Comparative genome and phylogenetic analysis demonstrated that phage ZH4 was highly similar to phages belonging to the genus Kayfunavirus. Moreover, the highest average nucleotide identity (ANI) values of phage ZH4 with all the known phages was 0.86, suggesting that ZH4 was a relatively novel phage. Temperature and pH stability tests showed that phage ZH4 was stable from 4° to 50 °C and pH range from 3 to 11. Host range of phage ZH4 showed that there were only 2 out of 17 strains lysed by phage ZH4. Taken together, phage ZH4 was considered as a novel phage with the potential for applications in the food and pharmaceutical industries.

Isolation and Characterization of Lytic Proteus Virus 309

Proteus mirabilis is frequently associated with complicated urinary tract infections (UTIs) and is the main cause of catheter-associated urinary tract infections (CAUTIs). Treatment of such infections is complicated and challenging due to the biofilm forming abilities of P. mirabilis. If neglected or mistreated, infections may lead to life-threating conditions such as cystitis, pyelonephritis, kidney failure, and bacteremia that may progress to urosepsis. Treatment with antibiotics, especially in cases of recurring and persistent infections, leads to the development of resistant strains. Recent insights into phage therapy and using phages to coat catheters have been evaluated with many studies showing promising results. Here, we describe a highly lytic bacteriophage, Proteus_virus_309 (41,740 bp), isolated from a wastewater treatment facility in Cape Town, South Africa. According to guidelines of the International Committee on Taxonomy of Viruses (ICTV), bacteriophage 309 is a species within the genus Novosibovirus. Similar to most members of the genus, bacteriophage 309 is strain-specific and lyse P. mirabilis in less than 20 min.

Synergistic Effects of Bacteriophage vB_Eco4-M7 and Selected Antibiotics on the Biofilm Formed by Shiga Toxin-Producing Escherichia coli

Apart from antibiotic resistance of pathogenic bacteria, the formation of biofilms is a feature that makes bacterial infections especially difficulty to treat. Shiga toxin-producing Escherichia coli (STEC) strains are dangerous pathogens, causing severe infections in humans, and capable of biofilm production. We have reported previously the identification and characterization of the vB_Eco4-M7 bacteriophage, infecting various STEC strains. It was suggested that this phage might be potentially used in phage therapy against these bacteria. Here, we tested the effects of vB_Eco4-M7 alone or in a phage cocktail with another STEC-infecting phage, and/or in a combination with different antibiotics (ciprofloxacin and rifampicin) on biofilm formed by a model STEC strain, named E. coli O157:H7 (ST2-8624). The vB_Eco4-M7 phage appeared effective in anti-biofilm action in all these experimental conditions (2–3-fold reduction of the biofilm density, and 2–3 orders of magnitude reduction of the number of bacterial cells). However, the highest efficiency in reducing a biofilm’s density and number of bacterial cells was observed when phage infection preceded antibiotic treatment (6-fold reduction of the biofilm density, and 5–6 orders of magnitude reduction of the number of bacterial cells). Previous reports indicated that the use of antibiotics to treat STEC-caused infections might be dangerous due to the induction of Shiga toxin-converting prophages from bacterial genomes under stress conditions caused by antibacterial agents. We found that ciprofloxacin was almost as efficient in inducing prophages from the E. coli O15:H7 (ST2-8624) genome as a classical inducer, mitomycin C, while no detectable prophage induction could be observed in rifampicin-treated STEC cells. Therefore, we conclude the latter antibiotic or similarly acting compounds might be candidate(s) as effective and safe drug(s) when used in combination with phage therapy to combat STEC-mediated infections.

Phage–Antibiotic Therapy as a Promising Strategy to Combat Multidrug-Resistant Infections and to Enhance Antimicrobial Efficiency

Infections caused by multidrug-resistant (MDR) bacteria have highlighted the importance of the development of new antimicrobial agents. While bacteriophages (phages) are widely studied as alternative agents to antibiotics, combined treatments using phages and antibiotics have exhibited Phage–Antibiotic Synergy (PAS), in which antibiotics promote phage replication and extraordinary antimicrobial efficacy with reduced development of bacterial resistance. This review paper on the current progress of phage–antibiotic therapy includes aspects of the mechanisms of PAS and the therapeutic performance of PAS in combating multidrug-resistant bacterial infections. The choice of phages and antibiotics, the administration time and sequence, and the concentrations of the two agents impact the bacterial inhibitory effects to different extents.

Phage-Antibiotic Synergy Inhibited by Temperate and Chronic Virus Competition

As antibiotic resistance grows more frequent for common bacterial infections, alternative treatment strategies such as phage therapy have become more widely studied in the medical field. While many studies have explored the efficacy of antibiotics, phage therapy, or synergistic combinations of phages and antibiotics, the impact of virus competition on the efficacy of antibiotic treatment has not yet been considered. Here, we model the synergy between antibiotics and two viral types, temperate and chronic, in controlling bacterial infections. We demonstrate that while combinations of antibiotic and temperate viruses exhibit synergy, competition between temperate and chronic viruses inhibits bacterial control with antibiotics. In fact, our model reveals that antibiotic treatment may counterintuitively increase the bacterial load when a large fraction of the bacteria are antibiotic resistant, and both chronic and temperate phages are present.

Isolation and Characterization of Lytic Bacteriophages Targeting Diverse Enterobacter spp. Clinical Isolates

Background: Enterobacter spp. are opportunistic pathogens that cause nosocomial infections. Bacteriophages could be used to treat antibiotic-resistant Enterobacter infections. Materials and Methods: We used 10 genetically diverse clinical Enterobacter spp. isolates to identify lytic bacteriophages in hospital and municipal wastewater. Comparative genomics was performed on host bacterial isolates and isolated phages. Activity of each phage against all 10 host isolates was determined. We also tested phage activity against paired isolates from two patients who developed ceftazidime-avibactam resistance. Results: Bacteria belonged to three Enterobacter species and Klebsiella aerogenes. We isolated 12 bacteriophages, most of which belonged to the Myoviridae and Autographiviridae families. Most phages were able to lyse multiple bacterial isolates, and many lysed isolates of different species. Ceftazidime-avibactam-resistant isolates were still phage susceptible, and one isolate showed increased susceptibility compared with the parent isolate. Conclusion: The phages we isolated expand the diversity of Enterobacter-targeting phages, and could be useful for treating antibiotic-resistant Enterobacter infections.

Bacteriophage Therapy for Critical and High-Priority Antibiotic-Resistant Bacteria and Phage Cocktail-Antibiotic Formulation Perspective

Phage therapy is revolving to address the issues mainly dealing with antibiotic resistance in the pathogenic bacteria. Among the drug-resistant microbial populations, the bacterial species have been categorized as high-priority or critical-priority bacteria. This review summarizes the efficiency and development in phage therapy used against these drug-resistant bacteria in the past few years mainly belonging to the critical- and high-priority list. Phage therapy is more than just an alternative to antibiotics as it not only kills the target microbial population directly but also leads to the chemical and physical modifications in bacterial cell structures. These phage-mediated modifications in the bacterial cell may make them antibiotic sensitive. Application of phage therapy in antibiotic-resistant foodborne bacteria and possible modulation in gut microbes has also been explored. Further, the phage cocktail antibiotic formulation, containing more than one type of phage with antibiotics, has also been discussed.