A comprehensive review of the applications of bacteriophage-derived endolysins for foodborne bacterial pathogens and food safety: recent advances, challenges, and future perspective

Endolysins and membrane-active peptides: innovative engineering strategies against gram-negative bacteria

Endolysins, bacteriophage-encoded peptidoglycan hydrolases, offer promising potential in antibacterial therapy, including treatments targeting gram-negative bacteria. While these enzymes naturally act primarily on gram-positive bacteria, their application against gram-negative pathogens is more challenging due to the presence of a dual-layer cell membrane, which acts as a protective barrier. However, innovative approaches, such as fusing endolysins with antimicrobial peptides (AMPs), have demonstrated increased efficacy against gram-negative bacteria. Modifying endolysins by introducing hydrophobic properties or positive charges or combining them with agents that disrupt the outer membrane enhances their bactericidal activity. Moreover, phage endolysins that exhibit activity against gram-negative bacteria are a promising source of membrane-active peptides. Identifying new peptide sequences derived from endolysins capable of penetrating the bacterial cell membrane represents a novel and increasingly explored research direction. Studying these innovative strategies had yielded promising results, though the field remains under active investigation and development. Ongoing efforts aim to optimize these approaches to improve their effectiveness against antibiotic-resistant gram-negative bacterial strains, which are particularly difficult to treat with conventional antibiotics. This review summarizes the latest advancements and solutions in the field, highlighting the potential of endolysins and membrane-active peptides as next-generation antibacterial agents.

Assessing the role of zinc in the structure-stability-activity paradigm of bacteriophage T7 endolysin

Inorganic cofactors, such as zinc, contribute to enzymatic reactions, protein folding, and enzyme stability. T7 endolysin or T7 lysozyme (T7L), a zinc-dependent amidase involved in the lysis of bacterial cell walls, has great potential for applications in biotechnology and medicine. The present study provides an in-depth analysis of the structure stability and catalytic features of T7L, focusing on the comparison of its Apo and Holo forms using turbidimetric assay, circular dichroism, fluorescence spectroscopy, nuclear magnetic resonance (NMR) spectroscopic methods and molecular dynamics simulations. T7L Apo and T7L Holo forms showed moderate structural differences in the secondary structure; hydrophobic exposure was observed at the tertiary level. Chemical denaturation studies indicated higher stability in T7L Holo compared to the Apo form. The pH-dependent NMR analyses implied the protective role of zinc in the Holo form at lower pH levels, down to pH 5. The turbidimetric assay further revealed the affirmative role of zinc as a cofactor for its amidase activity. Molecular dynamics simulation studies further ally with these results, demonstrating the secondary conformational stability of T7L Holo compared to the Apo form. T7L Holo exhibits dynamic interactions with the solvent water, underlining the flexible arrangements of bonds that drive the enhanced catalytic function of T7L Holo. These results provide insights into protein enzymology, emphasizing the crucial influence of cofactors on enzymatic reactions and protein stability. The distinct features of structure-stability-activity between Apo and Holo forms of T7L under various conditions pave the way for the development of strategies based on T7 endolysin to combat microbial resistance.

[Phage endolysins-a novel class of antibacterial agents with a wide range of applications]

As "enzybiotics," endolysins represent a new class of antibacterial agents that are naturally produced at the end of the lytic cycle in bacteriophage-infected bacterial cells to enable the phage particles formed to be released from the inside of the host cell. Their enzymatic effect on the cell wall peptidoglycan, which leads to lysis of the infected bacteria, can also be exerted externally as an applied agent. While the endolysin activity can be directly effective in Gram-positive bacteria, the endolysin must be modified for activity against Gram-negative bacteria so that it can overcome the outer cell membrane. For this reason, and to optimize endolysin specificity and stability, endolysins are increasingly being genetically modified and produced recombinantly, which is relatively easy to achieve due to their modular structure consisting of lytic and binding domains. Endolysins have already found increasing actual or extensively postulated use for preventive, therapeutic, and diagnostic purposes in human and veterinary medicine as well as in food safety, biotechnology, and the One Health sector; however, this still needs to be better substantiated by valid studies. Although, in contrast to phage therapy, the regulatory aspects can follow the approval procedures also required for other pharmaceuticals, only less than a dozen randomized controlled studies of phases 1 to 3 have been initiated or completed in the field of human medicine. Only very few endolysin formulations approved as medical products are currently available on the market and approval as medicinal drugs is being sought for some endolysins.

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 Endolysins as an Alternative Biocontrol Strategy for Pathogenic and Spoilage Microorganisms in the Food Industry

Food contamination by pathogenic and spoilage bacteria causes approximately 47 million cases of foodborne diseases in the United States and leads to tons of food spoilage, worsening the food loss situation worldwide. In addition, conventional preservation treatments implemented in the food industry decrease food's nutritional and organoleptic quality. Therefore, there is a need for new alternatives to counteract food contamination without altering its characteristics. Endolysins are a promising strategy due to their unique properties, such as host specificity, synergism with other antibacterial agents, mode of action, and low probability of resistance development. These characteristics differentiate them from other antibacterial agents used in the food industry. Endolysins are enzymes produced by bacteriophages during the process of bacterial infection and lysis. This review describes the advances related to endolysin application systems in food, considering their potential for food safety and an overview of the application conditions according to the type of food and bacteria to be controlled. We also highlight the need for new studies on endolysin encapsulation and prolongation of the action time in cases of outbreaks that allow obtaining key information to improve the application of endolysins in different food matrices during food processing and storage.

Phage Endolysins as Promising and Effective Candidates for Use Against Uropathogenic Escherichia coli

The presented in silico and phylogenetic analysis of putative endolysins potentially produced by phages infecting uropathogenic Escherichia coli (UPEC) demonstrates their remarkable diversity. These proteins exhibit significant variations in sequence length, molecular weight, isoelectric point, and stability, as well as diverse functional domains determining their enzymatic activity, including lysin, lysozyme, hydrolase, amidase, and peptidase functions. Due to their predicted lytic properties, endolysins hold great promise in combating UPEC bacteria, including those within biofilms, which are often highly resistant to conventional treatments. Despite their potential, several challenges hinder the full utilization of endolysins. These include the relatively small number of identified proteins, challenges in the annotation process, and the scarcity of studies evaluating their efficacy in vitro and in vivo against Gram-negative bacteria. In this work, we emphasize these challenges while also underlining the potential of endolysins as an effective tool against UPEC infections. Their effectiveness could be significantly enhanced when combined with agents that disrupt the outer membrane of these bacteria, making them a promising alternative or complement to existing antimicrobial strategies. Further research is necessary to fully explore their therapeutic potential.

Characterization of Clostridium perfringens Phage Endolysin PlyDolk21

Background:Clostridium perfringens is a significant cause of food poisoning. Broad-spectrum antibiotics, commonly used to control C. perfringens, are becoming less effective due to the rise of antibiotic-resistant strains, necessitating alternative control strategies. Methods: A C. perfringens-infecting bacteriophage, Dolk21, and its endolysin, PlyDolk21, were isolated and characterized. The lytic activity of PlyDolk21 was assessed in comparison to its catalytic domain alone. Both PlyDolk21 and its cell wall binding domain (CBD) were evaluated in beef and milk for their antimicrobial activity and cell wall binding activity, respectively. Results: While phage Dolk21 was specific to certain C. perfringens strains, PlyDolk21 exhibited lytic activity against all C. perfringens strains tested. The full-length PlyDolk21 showed stronger lytic activity compared to its catalytic domain alone. PlyDolk21_CBD successfully bound to C. perfringens in vitro and in foods. Additionally, PlyDolk21 effectively reduced the viable cell counts of C. perfringens by 3-log in beef soup and milk samples. Conclusions: This study demonstrates that PlyDolk21 and its CBD hold potential as a biocontrol and detection agent targeting C. perfringens in various food matrices.

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.

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.

Antibacterial mechanism of Lactiplantibacillus plantarum SHY96 cell-free supernatant against Listeria monocytogenes revealed by metabolomics and potential application on chicken breast meat preservation

The cell-free supernatant of Lactiplantibacillus plantarum (LCFS) is considered a potential natural antimicrobial agent due to its outstanding antimicrobial activity. This study demonstrated that the cell-free supernatant of L. plantarum SHY96 (LCFS96) effectively inhibits the growth and biofilm formation of L. monocytogenes CMCC(B)54002 (L. monocytogenes_02) by reducing cell metabolic activity and damaging cell structure. Metabolomic analysis revealed that LCFS96 significantly altered 450 intracellular metabolites, affecting key metabolic pathways including linoleic acid metabolism, pyrimidine metabolism, purine metabolism, pantothenic acid and CoA biosynthesis, and the TCA cycle. Additionally, application of LCFS96 significantly reduced L. monocytogenes_02 viable counts by 84.93%, while maintaining the pH, TVB-N and organoleptic properties of chicken meat under refrigeration at 4 °C for 12 days. These findings highlight the antimicrobial mechanism and potential application of LCFS96 in extending the shelf-life of meat products.

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.

Characterization of two Campylobacter jejuni phages and evaluation of their antibacterial efficacy with EDTA

Campylobacter jejuni is a leading cause of foodborne illness worldwide. The application of bacteriophages offers a promising approach to specifically target and reduce C. jejuni contamination in food products. In this study, two C. jejuni phages were characterized, and their ability to inhibit bacterial growth in combination with ethylenediaminetetraacetic acid (EDTA) was investigated. Both phages exhibited tolerance to a wide range of temperature (4-60 °C) and pH (3-9). Phage vB_CjeM-PC10 and vB_CjeM-PC22 were found to have a latent period of 30 min and 20 min and a burst size of 7 and 35 PFU/cell, respectively. Phage vB_CjeM-PC10 has a linear double-stranded DNA (dsDNA) genome of 51,148 bp with 77 ORFs and 29% GC content. Phage vB_CjeM-PC22 has a circular dsDNA genome of 32,543 bp with 56 ORFs and 28% GC content. At 42 °C, the combination of these phages (MOI = 10) and EDTA decreased the count of viable C. jejuni by 5.2 log10 and inhibited the regrowth of resistant cells for 48 h. At 4 °C, phage vB_CjeM-PC10 alone (MOI = 1000) reduced the count of viable C. jejuni by 3 log10 in brain heart infusion (BHI) broth and 2 log10 on chicken skin after incubation for 48 h. Although these phages were effective against C. jejuni, they cannot be utilized directly for food safety applications because they are lysogenic. Nevertheless, these findings expand the genome library of C. jejuni phages and enrich data resources by highlighting potential strategies for controlling C. jejuni infections.

Endolysins: a new antimicrobial agent against antimicrobial resistance. Strategies and opportunities in overcoming the challenges of endolysins against Gram-negative bacteria

Antibiotic-resistant bacteria are rapidly emerging, and the increasing prevalence of multidrug-resistant (MDR) Acinetobacter baumannii poses a severe threat to humans and healthcare organizations, due to the lack of innovative antibacterial drugs. Endolysins, which are peptidoglycan hydrolases encoded by a bacteriophage, are a promising new family of antimicrobials. Endolysins have been demonstrated as an effective therapeutic agent against bacterial infections of A. baumannii and many other Gram-positive and Gram-negative bacteria. Endolysin research has progressed from basic in vitro characterization to sophisticated protein engineering methodologies, including advanced preclinical and clinical testing. Endolysin are therapeutic agent that shows antimicrobial properties against bacterial infections caused by drug-resistant Gram-negative bacteria, there are still barriers to their implementation in clinical settings, such as safety concerns with outer membrane permeabilizers (OMP) use, low efficiency against stationary phase bacteria, and stability issues. The application of protein engineering and formulation techniques to improve enzyme stability, as well as combination therapy with other types of antibacterial drugs to optimize their medicinal value, have been reviewed as well. In this review, we summarize the clinical development of endolysin and its challenges and approaches for bringing endolysin therapies to the clinic. This review also discusses the different applications of endolysins.

Engineered endolysin of Klebsiella pneumoniae phage is a potent and broad-spectrum bactericidal agent against "ESKAPEE" pathogens

The rise of antimicrobial resistance in ESKAPEE pathogens poses significant clinical challenges, especially in polymicrobial infections. Bacteriophage-derived endolysins offer promise in combating this crisis, but face practical hurdles. Our study focuses on engineering endolysins from a Klebsiella pneumoniae phage, fusing them with ApoE23 and COG133 peptides. We assessed the resulting chimeric proteins' bactericidal activity against ESKAPEE pathogens in vitro. ApoE23-Kp84B (CHU-1) reduced over 3 log units of CFU for A. baumannii, E. faecalis, K. pneumoniae within 1 h, while COG133-Kp84B (CHU-2) showed significant efficacy against S. aureus. COG133-L1-Kp84B, with a GS linker insertion in CHU-2, exhibited outstanding bactericidal activity against E. cloacae and P. aeruginosa. Scanning electron microscopy revealed alterations in bacterial morphology after treatment with engineered endolysins. Notably, CHU-1 demonstrated promising anti-biofilm and anti-persister cell activity against A. baumannii and E. faecalis but had limited efficacy in a bacteremia mouse model of their coinfection. Our findings advance the field of endolysin engineering, facilitating the customization of these proteins to target specific bacterial pathogens. This approach holds promise for the development of personalized therapies tailored to combat ESKAPEE infections effectively.

Lysin and Lytic Phages Reduce Vibrio Counts in Live Feed and Fish Larvae

Vibrio species are naturally found in estuarine and marine ecosystems, but are also recognized as significant human enteropathogens, often linked to seafood-related illnesses. In aquaculture settings, Vibrio poses a substantial risk of infectious diseases, resulting in considerable stock losses and prompting the use of antimicrobials. However, this practice contributes to the proliferation of antimicrobial-resistant (AMR) bacteria and resistance genes. Our investigation aimed to explore the potential of biological agents such as bacteriophage CH20 and endolysin LysVPp1 in reducing Vibrio bacterial loads in both rotifer and fish larvae. LysVPp1's lytic activity was assessed by measuring absorbance reduction against various pathogenic Vibrio strains. Phage CH20 exhibited a limited host range, affecting only Vibrio alginolyticus GV09, a highly pathogenic strain. Both CH20 and LysVPp1 were evaluated for their effectiveness in reducing Vibrio load in rotifers or fish larvae through short-setting bioassays. Our results demonstrated the significant lytic effect of endolysin LysVPp1 on strains of Vibrio alginolyticus, Vibrio parahaemolyticus, and Vibrio splendidus. Furthermore, we have showcased the feasibility of reducing the load of pathogenic Vibrio in live feed and fish larvae by using a non-antibiotic-based approach, such as lytic phage and endolysin LysVPp1, thus contributing to the progress of a sustainable aquaculture from a One Health perspective.

Precision fermentation for improving the quality, flavor, safety, and sustainability of foods

Precision fermentation involves the rewiring of metabolic pathways in generally recognized as safe microorganisms, fermentation scale-up, and downstream processing to produce food ingredients from abundant and inexpensive substrates. Using precise genome editing of food-fermenting microorganisms, precision fermentation can also produce fermented foods with more desirable properties. These genetic tools allow for the manipulation of flavors and nutritional content in fermented foods, the economic production of functional food ingredients, and the sustainable production of otherwise-costly macronutrients. By introducing the metabolic designs, genetic modifications, and resulting products of engineered microorganisms developed through academic and industrial research, this review aims to provide insights into the potentials and challenges of precision fermentation for the economic, safe, and sustainable production of foods.