Phage Endolysins: Advances in the World of Food Safety

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.

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.

Phage-derived proteins: Advancing food safety through biocontrol and detection of foodborne pathogens

The emergence of antimicrobial-resistant foodborne pathogens poses a continuous health risk and economic burden as they can easily spread through contaminated food. Therefore, the demand for new antimicrobial agents to address this problem is steadily increasing. Similarly, the development of rapid, sensitive, and accurate pathogen detection tools is a prerequisite for ensuring food safety. Phage-derived proteins have become innovative tools for combating these pathogens because of their potent antimicrobial activity and host specificity. Phage proteins are relatively free from regulation compared to phages per se, and there are no concerns about the transduction of harmful genes. With recent progress in next-generation sequencing technology, the analysis of phage genomes has become more accessible, and numerous phage proteins with potential for biocontrol and detection have been identified. This review provides a comprehensive overview of phage protein research on food safety from 2006 to the present, a pivotal period marked by the certification of phages as Generally Recognized As Safe (GRAS). Emphasizing recent advancements, we investigated the diverse applications of various phage proteins for biocontrol and detection purposes. While highlighting the successful implementation of these proteins, we also address the current bottlenecks and propose strategies to overcome these challenges. By summarizing the current state of research on phage-derived proteins, this review contributes to a deeper understanding of their potential as effective antimicrobial agents and tools for detecting foodborne pathogens.

Characterization of the host specificity of the SH3 cell wall binding domain of the staphylococcal phage 88 endolysin

Bacteriophages produce endolysins at the end of the lytic cycle, which are crucial for lysing the host cells and releasing virion progeny. This lytic feature allows endolysins to act as effective antimicrobial alternatives when applied exogenously. Staphylococcal endolysins typically possess a modular structure with one or two enzymatically active N-terminal domains (EADs) and a C-terminal cell wall binding domain (CBD). The EADs degrade the peptidoglycan layer, leading to bacterial lysis, while the CBD binds to the specific host cell wall, and therefore, influences specificity of the endolysin. This study aimed to alter and characterize the host specificity of the CBD by exploring the impact of amino acid modifications within the CBD of a staphylococcal endolysin, Endo88. Endo88 was able to lyse Staphylococcus spp. and Enterococcus faecalis. However, despite attempts to mutate amino acids hypothesized for binding with cell wall components, the host-range was not affected but the lytic activity was severely reduced instead, although no alterations were performed on the EADs (Cysteine, histidine-dependent aminohydrolases/peptidases domain and Amidase domain). Further investigations of the CBD alone (Src homology3 domain, SH3) without the EADs suggested that binding and lytic activity may not be correlated in some cases since Endo88 and its mutants could lyse Staphylococcus epidermidis well but no binding activity was observed in the flow cytometry analysis. Molecular docking was used to gain insights on the observations for the binding and lytic activity which may help future strategies in designing enhanced engineered endolysins.

Phage-Derived Endolysins Against Resistant Staphylococcus spp.: A Review of Features, Antibacterial Activities, and Recent Applications

Antimicrobial resistance is a significant global public health issue, and the dissemination of antibiotic resistance in Gram-positive bacterial pathogens has significantly increased morbidity, mortality rates, and healthcare costs. Among them, Staphylococcus, especially methicillin-resistant Staphylococcus aureus (MRSA), causes a wide range of diseases due to its diverse pathogenic factors and infection strategies. These bacteria also present significant issues in veterinary medicine and food safety. Effectively managing staphylococci-related problems necessitates a concerted effort to implement preventive measures, rapidly detect the pathogen, and develop new and safe antimicrobial therapies. In recent years, there has been growing interest in using endolysins to combat bacterial infections. These enzymes, which are also referred to as lysins, are a unique class of hydrolytic enzymes synthesized by double-stranded DNA bacteriophages. They possess glycosidase, lytic transglycosylase, amidase, and endopeptidase activities, effectively destroying the peptidoglycan layer and resulting in bacterial lysis. This unique property makes endolysins powerful antimicrobial agents, particularly against Gram-positive organisms with more accessible peptidoglycan layers. Therefore, considering the potential benefits of endolysins compared to conventional antibiotics, we have endeavored to gather and review the characteristics and uses of endolysins derived from staphylococcal bacteriophages, as well as their antibacterial effectiveness against Staphylococcus spp. based on conducted experiments and trials.

Synergistic Enzybiotic Effect of a Bacteriophage Endolysin and an Engineered Glucose Oxidase Against Listeria

Listeria monocytogenes represents one of the main risks for food safety worldwide. Two enzyme-based antimicrobials (enzybiotics) have been combined in a novel treatment against this pathogenic bacterium, resulting in a powerful synergistic effect. One of the enzymes is an endolysin from Listeria phage vB_LmoS_188 with amidase activity (henceforth A10), and the other is an engineered version of glucose oxidase from Aspergillus niger (GOX). Both enzymes, assayed separately against Listeria innocua, showed antibacterial activity at the appropriate doses. The combination of the two enzybiotics resulted in a synergistic effect with a log reduction in viable cells (log N0/N) of 4, whereas, taken separately, the same dose of A10 and GOX caused only 1.2 and 0.2 log reductions, respectively. Flow cytometry and microscopy analyses revealed that A10 treatment alone induced the aggregation of dead cells. L. monocytogenes showed higher resistance to single treatment with GOX or A10 than L. innocua. However, the synergic combination of A10 and GOX resulted in a high lethality of L. monocytogenes with a log N0/N higher than 5 (below the detection limit in our analysis). Altogether, these results represent a novel efficient and eco-friendly antimicrobial treatment against the most lethal food-borne pathogen.

Molecular Docking of Endolysins for Studying Peptidoglycan Binding Mechanism

Endolysins of bacteriophages, which degrade the bacterial cell wall peptidoglycan, are applicable in many industries to deal with biofilms and bacterial infections. While multi-domain endolysins have both enzymatically active and cell wall-binding domains, single-domain endolysins consist only of an enzymatically active domain, and their mechanism of peptidoglycan binding remains unexplored, for this is a challenging task experimentally. This research aimed to explore the binding mechanism of endolysins using computational approaches, namely molecular docking and bioinformatical tools, and analyze the performance of these approaches. The docking engine Autodock Vina 1.1.2 and the 3D-RISM module of AmberTools 24 were studied in the current work and used for receptor-ligand affinity and binding energy calculations, respectively. Two possible mechanisms of single-domain endolysin-ligand binding were predicted by Autodock Vina and verified by the 3D-RISM. As a result, the previously obtained experimental results on peptidoglycan binding of the isolated gamma phage endolysin PlyG enzymatically active domain were supported by molecular docking. Both methods predicted that single-domain endolysins are able to bind peptidoglycan, with Autodock Vina being able to give accurate numerical estimates of protein-ligand affinities and 3D-RISM providing comparative values.

Bacteriophage as a potential biotherapeutics to combat present-day crisis of multi-drug resistant pathogens

The rise of Multi-Drug Resistant (MDR) bacterial pathogens to most, if not all, currently available antibacterial agents has become a global threat. As a consequence of the antibiotic resistance epidemic, phage therapy has emerged as a potential alternative to conventional antibiotics. Despite the high therapeutic advantages of phage therapy, they have not yet been successfully used in the clinic due to various limitations of narrow host specificity compared to antibiotics, poor adhesion on biofilm surface, and susceptibility to both human and bacterial defences. This review focuses on the antibacterial effect of bacteriophage and their recent clinical trials with a special emphasis on the underlying mechanism of lytic phage action with the help of endolysin and holin. Furthermore, recent clinical trials of natural and modified endolysins and some marketed products have also been emphasized with future prospective.

Activity and safety evaluation of natural preservatives

Synthetic preservatives are widely used in the food industry to control spoilage and growth of pathogenic microorganisms, inhibit lipid oxidation processes and extend the shelf life of food. However, synthetic preservatives have some side effects that can lead to poisoning, cancer and other degenerative diseases. With the improvement of living standards, people are developing safer natural preservatives to replace synthetic preservatives, including plant derived preservatives (polyphenols, essential oils, flavonoids), animal derived preservatives (lysozyme, antimicrobial peptide, chitosan) and microorganism derived preservatives (nisin, natamycin, ε-polylysine, phage). These natural preservatives exert antibacterial effects by disrupting microbial cell wall/membrane structures, interfering with DNA/RNA replication and transcription, and affecting protein synthesis and metabolism. This review summarizes the natural bioactive compounds (polyphenols, flavonoids and terpenoids, etc.) in these preservatives, their antioxidant and antibacterial activities, and safety evaluation in various products.

Analyzing the impact of T7L variants overexpression on the metabolic profile of Escherichia coli

INTRODUCTION

Exploring metabolic changes within host E. coli through an untargeted metabolomic study of T7L variants overexpression to optimize engineered endolysins for clinical/therapeutic use.

AIM AND OBJECTIVE

This study aims to assess the impact of overexpressing T7L variants on the metabolic profiles of E. coli. The two variants considered include T7L-H37A, which has enhanced lytic activity compared to its wild-type protein, and T7L-H48K, a dead mutant with no significant activity.

METHODS

1H NMR-based metabolomics was employed to compare the metabolic profiles of E. coli cells overexpressing T7L wild-type protein and its variants.

RESULTS

Overexpression of the T7L wild-type (T7L-WT) protein and its variants (T7L-H48K and T7L-H37A) was compared to RNAP overexpression in E. coli cells using 1H NMR-based metabolomics, analyzing a total of 75 annotated metabolites, including organic acids, amino acids, sugars, and nucleic acids. The results showed distinct clustering patterns for the two T7L variant groups compared with the WT, in which the dead mutant (H48K) group showed clustering close to that of RNAP. Pathway impact analysis revealed different effects of T7L variants on E. coli metabolic profiles, with T7L-H48K showing minimal alterations in energy and amino acid pathways linked to osmotic stress compared to noticeable alterations in these pathways for both T7L-H37A and T7L-WT.

CONCLUSIONS

This study uncovered distinct metabolic fingerprints when comparing the overexpression of active and inactive mutants of T7L lytic enzymes in E. coli cells. These findings could contribute to the optimization and enhancement of suitable endolysins as potential alternatives to antibiotics.

Bacteriophages of Thermophilic 'Bacillus Group' Bacteria-A Systematic Review, 2023 Update

Bacteriophages associated with thermophiles are gaining increased attention due to their pivotal roles in various biogeochemical and ecological processes, as well as their applications in biotechnology and bionanotechnology. Although thermophages are not suitable for controlling bacterial infections in humans or animals, their individual components, such as enzymes and capsid proteins, can be employed in molecular biology and significantly contribute to the enhancement of human and animal health. Despite their significance, thermophages still remain underrepresented in the known prokaryotic virosphere, primarily due to limited in-depth investigations. However, due to their unique properties, thermophages are currently attracting increasing interest, as evidenced by several newly discovered phages belonging to this group. This review offers an updated compilation of thermophages characterized to date, focusing on species infecting the thermophilic bacilli. Moreover, it presents experimental findings, including novel proteomic data (39 proteins) concerning the model TP-84 bacteriophage, along with the first announcement of 6 recently discovered thermophages infecting Geobacillus thermodenitrificans: PK5.2, PK2.1, NIIg10.1, NIIg2.1, NIIg2.2, and NIIg2.3. This review serves as an update to our previous publication in 2021.

Phytopathological management through bacteriophages: enhancing food security amidst climate change

The increasing global population and climate change pose significant challenges to agriculture, particularly in managing plant diseases caused by phytopathogens. Traditional methods, including chemical pesticides and antibiotics, have become less effective due to pathogen resistance and environmental concerns. Phage therapy emerges as a promising alternative, offering a sustainable and precise approach to controlling plant bacterial diseases without harming beneficial soil microorganisms. This review explores the potential of bacteriophages as biocontrol agents, highlighting their specificity, rapid multiplication, and minimal environmental impact. We discuss the historical context, current applications, and prospects of phage therapy in agriculture, emphasizing its role in enhancing crop yield and quality. Additionally, the paper examines the integration of phage therapy with modern agricultural practices and the development phage cocktails and genetically engineered phages to combat resistant pathogens. The findings suggest that phage therapy could revolutionize phytopathological management, contributing to global food security and sustainable agricultural practices.

ONE-SENTENCE SUMMARY

The burden of plant diseases and phage-based phytopathological treatment.