Role of net charge on catalytic domain and influence of cell wall binding domain on bactericidal activity, specificity, and host range of phage lysins

Uncovering Endolysins against Methicillin-Resistant Staphylococcus aureus Using a Microbial Single-Cell Genome Database

Endolysins, peptidoglycan hydrolases derived from bacteriophages (phages), are being developed as a promising alternative to conventional antibiotics. To obtain highly active endolysins, a diverse library of these endolysins is vital. We propose here microbial single-cell genome sequencing as an efficient tool to discover dozens of previously unknown endolysins, owing to its culture-independent sequencing method. As a proof of concept, we analyzed and recovered endolysin genes within prophage regions of Staphylococcus single-amplified genomes in human skin microbiome samples. We constructed a library of chimeric endolysins by shuffling domains of the natural endolysins and performed high-throughput screening against Staphylococcus aureus. One of the lead endolysins, bbst1027, exhibited desirable antimicrobial properties, such as rapid bactericidal activity, no detectable resistance development, and in vivo efficacy. We foresee that this endolysin discovery pipeline is in principle applicable to any bacterial target and boost the development of novel antimicrobial agents.

Engineered bacteriophages: A panacea against pathogenic and drug resistant bacteria

Antimicrobial resistance (AMR) is a major global concern; antibiotics and other regular treatment methods have failed to overcome the increasing number of infectious diseases. Bacteriophages (phages) are viruses that specifically target/kill bacterial hosts without affecting other human microbiome. Phage therapy provides optimism in the current global healthcare scenario with a long history of its applications in humans that has now reached various clinical trials. Phages in clinical trials have specific requirements of being exclusively lytic, free from toxic genes with an enhanced host range that adds an advantage to this requisite. This review explains in detail the various phage engineering methods and their potential applications in therapy. To make phages more efficient, engineering has been attempted using techniques like conventional homologous recombination, Bacteriophage Recombineering of Electroporated DNA (BRED), clustered regularly interspaced short palindromic repeats (CRISPR)-Cas, CRISPY-BRED/Bacteriophage Recombineering with Infectious Particles (BRIP), chemically accelerated viral evolution (CAVE), and phage genome rebooting. Phages are administered in cocktail form in combination with antibiotics, vaccines, and purified proteins, such as endolysins. Thus, phage therapy is proving to be a better alternative for treating life-threatening infections, with more specificity and fewer detrimental consequences.

You get what you test for: The killing effect of phage lysins is highly dependent on buffer tonicity and ionic strength

The phage lysin field has done nothing but grow in the last decades. As a result, many different research groups around the world are contributing to the field, often with certain methodological differences that pose a challenge to the interpretation and comparison of results. In this work, we present the case study of three Acinetobacter baumannii-targeting phage lysins (wild-type endolysin LysMK34 plus engineered lysins eLysMK34 and 1D10) plus one lysin with broad activity against Gram-positive bacteria (PlySs2) to provide exemplary evidence on the risks of generalization when using one of the most common lysin evaluation assays: the killing assay with resting cells. To that end, we performed killing assays with the aforementioned lysins using hypo-, iso- and hypertonic buffers plus human serum either as the reaction or the dilution medium in a systematic manner. Our findings stress the perils of creating hypotonic conditions or a hypotonic shock during a killing assay, suggesting that hypotonic buffers should be avoided as a test environment or as diluents before plating to avoid overestimation of the killing effect in the assayed conditions. As a conclusion, we suggest that the nature of both the incubation and the dilution buffers should be always clearly identified when reporting killing activity data, and that for experimental consistency the same incubation buffer should be used as a diluent for posterior serial dilution and plating unless explicitly required by the experimental design. In addition, the most appropriate buffer mimicking the final application must be chosen to obtain relevant results.

Lysins as a powerful alternative to combat Bacillus anthracis

This review gathers all, to the best of our current knowledge, known lysins, mainly bacteriophage-derived, that have demonstrated activity against Bacillus anthracis strains. B. anthracis is a spore-forming, toxin-producing bacteria, naturally dwelling in soil. It is best known as a potential biowarfare threat, an etiological agent of anthrax, and a severe zoonotic disease. Anthrax can be treated with antibiotics (ciprofloxacin, penicillin, doxycycline); however, their administration may take up even to 60 days, and different factors can compromise their effectiveness. Bacterial viruses, bacteriophages (phages), are natural enemies of bacteria and use their lytic enzymes, endolysins (lysins), to specifically kill bacterial cells. Harnessing the potential of lysins to combat bacterial infections holds promise for diminishing antibiotic usage and, consequently, addressing the escalating antibiotic resistance in bacteria. In this context, we list the lysins with the activity against B. anthracis, providing a summary of their lytic properties in vitro and the outcomes observed in animal models. Bacillus cereus strain ATCC 4342/RSVF1, a surrogate for B. anthracis, was also included as a target bacteria. KEY POINTS: • More than a dozen different B. anthracis lysins have been identified and studied. • They fall into three blocks regarding their amino acid sequence similarity and most of them are amidases. • Lysins could be used in treating B. anthracis infections.

Engineering of chimeric enzymes with expanded tolerance to ionic strength

Antimicrobial resistance poses a significant global threat, reaching dangerously high levels as reported by the World Health Organization. The emergence and rapid spread of new resistance mechanisms, coupled with the absence of effective treatments in recent decades, have led to thousands of deaths annually from infections caused by drug-resistant microorganisms. Consequently, there is an urgent need for the development of new compounds capable of combating antibiotic-resistant bacteria. A promising class of molecules exhibiting potent bactericidal effects is peptidoglycan hydrolases. Previously, we cloned and characterized the biochemical properties of the M23 catalytic domain of the EnpA (EnpACD) protein from Enterococcus faecalis. Unlike other enzymes within the M23 family, EnpACD demonstrates broad specificity. However, its activity is constrained under low ionic strength conditions. In this study, we present the engineering of three chimeric enzymes comprising EnpACD fused with three distinct SH3b cell wall-binding domains. These chimeras exhibit enhanced tolerance to environmental conditions and sustained activity in bovine and human serum. Furthermore, our findings demonstrate that the addition of SH3b domains influences the activity of the chimeric enzymes, thereby expanding their potential applications in combating antimicrobial resistance.IMPORTANCEThese studies demonstrate that the addition of the SH3b-binding domain to the EnpACD results in generation of chimeras with a broader tolerance to ionic strength and pH values, enabling them to remain active over a wider range of conditions. Such approach offers a relatively straightforward method for obtaining antibacterial enzymes with tailored properties and emphasizes the potential for proteins' engineering with enhanced functionality, contributing to the ongoing efforts to address antimicrobial resistance effectively.

Decoding the Structure-Function Relationship of the Muramidase Domain in E. coli O157.H7 Bacteriophage Endolysin: A Potential Building Block for Chimeric Enzybiotics

Bacteriophage endolysins are potential alternatives to conventional antibiotics for treating multidrug-resistant gram-negative bacterial infections. However, their structure-function relationships are poorly understood, hindering their optimization and application. In this study, we focused on the individual functionality of the C-terminal muramidase domain of Gp127, a modular endolysin from E. coli O157:H7 bacteriophage PhaxI. This domain is responsible for the enzymatic activity, whereas the N-terminal domain binds to the bacterial cell wall. Through protein modeling, docking experiments, and molecular dynamics simulations, we investigated the activity, stability, and interactions of the isolated C-terminal domain with its ligand. We also assessed its expression, solubility, toxicity, and lytic activity using the experimental data. Our results revealed that the C-terminal domain exhibits high activity and toxicity when tested individually, and its expression is regulated in different hosts to prevent self-destruction. Furthermore, we validated the muralytic activity of the purified refolded protein by zymography and standardized assays. These findings challenge the need for the N-terminal binding domain to arrange the active site and adjust the gap between crucial residues for peptidoglycan cleavage. Our study shed light on the three-dimensional structure and functionality of muramidase endolysins, thereby enriching the existing knowledge pool and laying a foundation for accurate in silico modeling and the informed design of next-generation enzybiotic treatments.

Review on sterilization techniques, and the application potential of phage lyase and lyase immobilization in fighting drug-resistant bacteria

Many human health problems and property losses caused by pathogenic contamination cannot be underestimated. Bactericidal techniques have been extensively studied to address this issue of public health and economy. Bacterial resistance develops as a result of the extensive use of single or multiple but persistent usage of sterilizing drugs, and the emergence of super-resistant bacteria brings new challenges. Therefore, it is crucial to control pathogen contamination by applying innovative and effective sterilization techniques. As organisms that exist in nature and can specifically kill bacteria, phages have become the focus as an alternative to antibacterial agents. Furthermore, phage-encoded lyases are proteins that play important roles in phage sterilization. The in vitro sterilization of phage lyase has been developed as a novel biosterilization technique to reduce bacterial resistance and is more environmentally friendly than conventional sterilization treatments. For the shortcomings of enzyme applications, this review discusses the enzyme immobilization methods and the application potential of immobilized lyases for sterilization. Although some techniques provide effective solutions, immobilized lyase sterilization technology has been proven to be a more effective innovation for efficient pathogen killing and reducing bacterial resistance. We hope that this review can provide new insights for the development of sterilization techniques.

Antibacterial synergy between a phage endolysin and citric acid against the Gram-negative kiwifruit pathogen Pseudomonas syringae pv. actinidiae

Horticultural diseases caused by bacterial pathogens provide an obstacle to crop production globally. Management of the infection of kiwifruit by the Gram-negative phytopathogen Pseudomonas syringae pv. actinidiae (Psa) currently includes copper and antibiotics. However, the emergence of bacterial resistance and a changing regulatory landscape are providing the impetus to develop environmentally sustainable antimicrobials. One potential strategy is the use of bacteriophage endolysins, which degrade peptidoglycan during normal phage replication, causing cell lysis and the release of new viral progeny. Exogenous use of endolysins as antimicrobials is impaired by the outer membrane of Gram-negative bacteria that provides an impermeable barrier and prevents endolysins from accessing their target peptidoglycan. Here, we describe the synergy between citric acid and a phage endolysin, which results in a reduction of viable Psa below detection. We show that citric acid drives the destabilization of the outer membrane via acidification and sequestration of divalent cations from the lipopolysaccharide, which is followed by the degradation of the peptidoglycan by the endolysin. Scanning electron microscopy revealed clear morphological differences, indicating cell lysis following the endolysin-citric acid treatment. These results show the potential for citric acid-endolysin combinations as a possible antimicrobial approach in agricultural applications.

IMPORTANCE

The phytopathogen Pseudomonas syringae pv. actinidiae (Psa) causes major impacts to kiwifruit horticulture, and the current control strategies are heavily reliant on copper and antibiotics. The environmental impact and increasing resistance to these agrichemicals are driving interest in alternative antimicrobials including bacteriophage-derived therapies. In this study, we characterize the endolysin from the Otagovirus Psa374 which infects Psa. When combined with citric acid, this endolysin displays an impressive antibacterial synergy to reduce viable Psa below the limit of detection. The use of citric acid as a synergistic agent with endolysins has not been extensively studied and has never been evaluated against a plant pathogen. We determined that the synergy involved a combination of the chelation activity of citric acid, acidic pH, and the specific activity of the ΦPsa374 endolysin. Our study highlights an exciting opportunity for alternative antimicrobials in agriculture.

Characterization and complete genome analysis of Klebsiella phage Kp109 with lytic activity against Klebsiella pneumoniae

Klebsiella pneumonia is a serious pathogen involved in a range of infections. The increasing frequency of infection associated with K. pneumoniae and accelerated development of antimicrobial resistance has limited the available options of antibiotics for the treatment of infection. Bacteriophages are an attractive substitute to alleviate the problem of antibiotic resistance. In this study, isolation, microbiological and genomic characterization of bacteriophage Kp109 having the ability to infect K. pneumoniae has been shown. Phage Kp109 showed good killing efficiency and tolerance to a broad range of temperatures (4-60 °C) and pH (3-9). Transmission electron microscopy and genomic analysis indicated that phage Kp109 belongs to the genus Webervirus and family Drexlerviridae. Genomic analysis showed that the Kp109 has a 51,630 bp long double-stranded DNA genome with a GC content of 51.64%. The absence of known lysogenic, virulence, and antibiotic-resistant genes (ARGs) in its genome makes phage Kp109 safer to be used as a biocontrol agent for different purposes including phage therapy. The computational analysis of the putative endolysin gene revealed a binding energy of - 6.23 kcal/mol between LysKp109 and ligand NAM-NAG showing its potential to be used as an enzybiotic. However, future research is required for experimental validation of the in silico work to further corroborate the results obtained in the present study. Overall, phenotypic, genomic, and computational characterization performed in the present study showed that phages Kp109 and LysKp109 are promising candidates for future in vivo studies and could potentially be used for controlling K. pneumoniae infection.

Metagenomic analysis of hot spring soil for mining a novel thermostable enzybiotic

The misuse and overuse of antibiotics have contributed to a rapid emergence of antibiotic-resistant bacterial pathogens. This global health threat underlines the urgent need for innovative and novel antimicrobials. Endolysins derived from bacteriophages or prophages constitute promising new antimicrobials (so-called enzybiotics), exhibiting the ability to break down bacterial peptidoglycan (PG). In the present work, metagenomic analysis of soil samples, collected from thermal springs, allowed the identification of a prophage-derived endolysin that belongs to the N-acetylmuramoyl-L-alanine amidase type 2 (NALAA-2) family and possesses a LysM (lysin motif) region as a cell wall binding domain (CWBD). The enzyme (Ami1) was cloned and expressed in Escherichia coli, and its bactericidal and lytic activity was characterized. The results indicate that Ami1 exhibits strong bactericidal and antimicrobial activity against a broad range of bacterial pathogens, as well as against isolated peptidoglycan (PG). Among the examined bacterial pathogens, Ami1 showed highest bactericidal activity against Staphylococcus aureus sand Staphylococcus epidermidis cells. Thermostability analysis revealed a melting temperature of 64.2 ± 0.6 °C. Overall, these findings support the potential that Ami1, as a broad spectrum antimicrobial agent, could be further assessed as enzybiotic for the effective treatment of bacterial infections. KEY POINTS: • Metagenomic analysis allowed the identification of a novel prophage endolysin • The endolysin belongs to type 2 amidase family with lysin motif region • The endolysin displays high thermostability and broad bactericidal spectrum.

Characterization of a Thermostable Endolysin of the Aeribacillus Phage AeriP45 as a Potential Staphylococcus Biofilm-Removing Agent

Multidrug-resistant Gram-positive bacteria, including bacteria from the genus Staphylococcus, are currently a challenge for medicine. Therefore, the development of new antimicrobials is required. Promising candidates for new antistaphylococcal drugs are phage endolysins, including endolysins from thermophilic phages against other Gram-positive bacteria. In this study, the recombinant endolysin LysAP45 from the thermophilic Aeribacillus phage AP45 was obtained and characterized. The recombinant endolysin LysAP45 was produced in Escherichia coli M15 cells. It was shown that LysAP45 is able to hydrolyze staphylococcal peptidoglycans from five species and eleven strains. Thermostability tests showed that LysAP45 retained its hydrolytic activity after incubation at 80 °C for at least 30 min. The enzymatically active domain of the recombinant endolysin LysAP45 completely disrupted biofilms formed by multidrug-resistant S. aureus, S. haemolyticus, and S. epidermidis. The results suggested that LysAP45 is a novel thermostable antimicrobial agent capable of destroying biofilms formed by various species of multidrug-resistant Staphylococcus. An unusual putative cell-binding domain was found at the C-terminus of LysAP45. No domains with similar sequences were found among the described endolysins.

New treatment approaches for Clostridioides difficile infections: alternatives to antibiotics and fecal microbiota transplantation

Clostridioides difficile causes a range of debilitating intestinal symptoms that may be fatal. It is particularly problematic as a hospital-acquired infection, causing significant costs to the health care system. Antibiotics, such as vancomycin and fidaxomicin, are still the drugs of choice for C. difficile infections, but their effectiveness is limited, and microbial interventions are emerging as a new treatment option. This paper focuses on alternative treatment approaches, which are currently in various stages of development and can be divided into four therapeutic strategies. Direct killing of C. difficile (i) includes beside established antibiotics, less studied bacteriophages, and their derivatives, such as endolysins and tailocins. Restoration of microbiota composition and function (ii) is achieved with fecal microbiota transplantation, which has recently been approved, with standardized defined microbial mixtures, and with probiotics, which have been administered with moderate success. Prevention of deleterious effects of antibiotics on microbiota is achieved with agents for the neutralization of antibiotics that act in the gut and are nearing regulatory approval. Neutralization of C. difficile toxins (iii) which are crucial virulence factors is achieved with antibodies/antibody fragments or alternative binding proteins. Of these, the monoclonal antibody bezlotoxumab is already in clinical use. Immunomodulation (iv) can help eliminate or prevent C. difficile infection by interfering with cytokine signaling. Small-molecule agents without bacteriolytic activity are usually selected by drug repurposing and can act via a variety of mechanisms. The multiple treatment options described in this article provide optimism for the future treatment of C. difficile infection.

Design strategies for positively charged endolysins: Insights into Artilysin development

Endolysins are bacteriophage-encoded enzymes that can specifically degrade the peptidoglycan layer of bacterial cell wall, making them an attractive tool for the development of novel antibacterial agents. The use of genetic engineering techniques for the production and modification of endolysins offers the opportunity to customize their properties and activity against specific bacterial targets, paving the way for the development of personalized therapies for bacterial infections. Gram-negative bacteria possess an outer membrane that can hinder the action of recombinantly produced endolysins. However, certain endolysins are capable of crossing the outer membrane by virtue of segments that share properties resembling those of cationic peptides. These regions increase the affinity of the endolysin towards the bacterial surface and assist in the permeabilization of the membrane. In order to improve the bactericidal effectiveness of endolysins, approaches have been implemented to increase their net charge, including the development of Artilysins containing positively charged amino acids at one end. At present, there are no specific guidelines outlining the steps for implementing these modifications. There is an ongoing debate surrounding the optimal location of positive charge, the need for a linker region, and the specific amino acid composition of peptides for modifying endolysins. The aim of this study is to provide clarity on these topics by analyzing and comparing the most effective modifications found in previous literature.

Two novel Bartonella (sub)species isolated from edible dormice (Glis glis): hints of cultivation stress-induced genomic changes

Bartonelloses are neglected emerging infectious diseases caused by facultatively intracellular bacteria transmitted between vertebrate hosts by various arthropod vectors. The highest diversity of Bartonella species has been identified in rodents. Within this study we focused on the edible dormouse (Glis glis), a rodent with unique life-history traits that often enters households and whose possible role in the epidemiology of Bartonella infections had been previously unknown. We identified and cultivated two distinct Bartonella sub(species) significantly diverging from previously described species, which were characterized using growth characteristics, biochemical tests, and various molecular techniques including also proteomics. Two novel (sub)species were described: Bartonella grahamii subsp. shimonis subsp. nov. and Bartonella gliris sp. nov. We sequenced two individual strains per each described (sub)species. During exploratory genomic analyses comparing two genotypes ultimately belonging to the same species, both factually and most importantly even spatiotemporally, we noticed unexpectedly significant structural variation between them. We found that most of the detected structural variants could be explained either by prophage excision or integration. Based on a detailed study of one such event, we argue that prophage deletion represents the most probable explanation of the observed phenomena. Moreover, in one strain of Bartonella grahamii subsp. shimonis subsp. nov. we identified a deletion related to Bartonella Adhesin A, a major pathogenicity factor that modulates bacteria-host interactions. Altogether, our results suggest that even a limited number of passages induced sufficient selective pressure to promote significant changes at the level of the genome.

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

Foodborne diseases are caused by food contaminated by pathogenic bacteria such as Escherichia coli, Salmonella, Staphylococcus aureus, Listeria monocytogenes, Campylobacter, and Clostridium, a critical threat to human health. As a novel antibacterial agent against foodborne pathogens, endolysins are peptidoglycan hydrolases encoded by bacteriophages that lyse bacterial cells by targeting their cell wall, notably in Gram-positive bacteria due to their naturally exposed peptidoglycan layer. These lytic enzymes have gained scientists' interest in recent years due to their selectivity, mode of action, engineering potential, and lack of resistance mechanisms. The use of endolysins for food safety has undergone significant improvements, which are summarized and discussed in this review. Endolysins can remove bacterial biofilms of foodborne pathogens and their cell wall-binding domain can be employed as a tool for quick detection of foodborne pathogens. We explained the applications of endolysin for eliminating pathogenic bacteria in livestock and various food matrices, as well as the limitations and challenges in use as a dietary supplement. We also highlight the novel techniques of the development of engineering endolysin for targeting Gram-negative bacterial pathogens. In conclusion, endolysin is safe and effective against foodborne pathogens and has no adverse effect on human cells and beneficial microbiota. As a result, endolysin could be employed as a functional bio-preservative agent to improve food stability and safety and maintain the natural taste of food quality.

Evaluating the efficacy of endolysins and membrane permeabilizers against Vibrio parahaemolyticus in marine conditions

Endolysins have garnered significant attention as a potential alternative to antibiotics in aquaculture, mainly for combating Vibrio spp., Gram-negative pathogens responsible for infectious outbreaks. However, endolysin effectiveness against Gram-negative bacteria is limited due to the outer membrane's poor permeability. The combat against marine pathogens poses an additional challenge of finding endolysins that retain their activity in high ionic strength conditions. Thus, this study aimed to demonstrate that certain endolysins retain muralytic activity in seawater and also evaluated outer membrane permeabilizers as endolysin adjuvants. The effectiveness of KZ144 and LysPA26 endolysins, along with EDTA and oregano essential oil, was evaluated against Vibrio parahaemolyticus ATCC-17802 in natural seawater. Results revealed the muralytic activity of both endolysins in seawater. However, the endolysins appeared to counteract the permeabilizers' effect during the initial bactericidal assays. Further investigations revealed that the observed effect was not antagonistic. After the permeabilizer action, V. parahaemolyticus likely used endolysins as a growth substrate. Endolysins may not play an indifferent role if they fail to exert a bactericidal effect. Instead, they can serve as a substrate for fast-growing bacteria, such as V. parahaemolyticus, increasing bacterial density. It should be considered a potential drawback of endolysins' proteinaceous nature as bactericidal agents.

Phage Endolysins: Advances in the World of Food Safety

As antimicrobial resistance continues to escalate, the exploration of alternative approaches to safeguard food safety becomes more crucial than ever. Phage endolysins are enzymes derived from phages that possess the ability to break down bacterial cell walls. They have emerged as promising antibacterial agents suitable for integration into food processing systems. Their application as food preservatives can effectively regulate pathogens, thus contributing to an overall improvement in food safety. This review summarizes the latest techniques considering endolysins' potential for food safety. These techniques include native and engineered endolysins for controlling bacterial contamination at different points within the food production chain. However, we find that characterizing endolysins through in vitro methods proves to be time consuming and resource intensive. Alternatively, the emergence of advanced high-throughput sequencing technology necessitates the creation of a robust computational framework to efficiently characterize recently identified endolysins, paving the way for future research. Machine learning encompasses potent tools capable of analyzing intricate datasets and pattern recognition. This study briefly reviewed the use of these industry 4.0 technologies for advancing the research in food industry. We aimed to provide current status of endolysins in food industry and new insights by implementing these industry 4.0 strategies revolutionizes endolysin development. It will enhance food safety, customization, efficiency, transparency, and collaboration while reducing regulatory hurdles and ensuring timely product availability.

LysGR1, a novel thermostable endolysin from Geobacillus stearothermophilus bacteriophage GR1

Geobacillus stearothermophilus is a highly thermophilic, spore-forming Gram-positive bacterium that causes flat sour spoilage in low-acid canned foods. To address this problem, we isolated G. stearothermophilus-infecting phage GR1 from the soil and characterized its endolysin LysGR1. Phage GR1 belongs to the Siphoviridae family and possesses a genome of 79,387 DNA bps with 108 putative open reading frames. GR1 demonstrated a very low degree of homology to previously reported phages, indicating that it is novel. The endolysin of GR1 (LysGR1) contains an N-terminal amidase domain as an enzymatically active domain (EAD) and two C-terminal LysM domains as a cell wall binding domain (CBD). Although GR1 is specific to certain strains of G. stearothermophilus, LysGR1 showed a much broader lytic range, killing all the tested strains of G. stearothermophilus and several foodborne pathogens, such as Clostridium perfringens, Listeria monocytogenes, and Escherichia coli O157:H7. LysGR1_EAD, alone, also exhibits lytic activity against a wide range of bacteria, including Bacillus cereus, which is not terminated by a full-length endolysin. Both LysGR1 and its EAD effectively remove the G. stearothermophilus biofilms and are highly thermostable, retaining about 70% of their lytic activity after a 15-min incubation at 70°C. Considering the high thermal stability, broad lytic activity, and biofilm reduction efficacy of LysGR1 and its EAD, we hypothesize that these enzymes could act as promising biocontrol agents against G. stearothermophilus and as foodborne pathogens.

Characterization and Engineering Studies of a New Endolysin from the Propionibacterium acnes Bacteriophage PAC1 for the Development of a Broad-Spectrum Artilysin with Altered Specificity

The emergence of multidrug-resistant (MDR) bacteria has risen rapidly, leading to a great threat to global public health. A promising solution to this problem is the exploitation of phage endolysins. In the present study, a putative N-acetylmuramoyl-L-alanine type-2 amidase (NALAA-2, EC 3.5.1.28) from Propionibacterium bacteriophage PAC1 was characterized. The enzyme (PaAmi1) was cloned into a T7 expression vector and expressed in E. coli BL21 cells. Kinetics analysis using turbidity reduction assays allowed the determination of the optimal conditions for lytic activity against a range of Gram-positive and negative human pathogens. The peptidoglycan degradation activity of PaAmi1 was confirmed using isolated peptidoglycan from P. acnes. The antibacterial activity of PaAmi1 was investigated using live P. acnes cells growing on agar plates. Two engineered variants of PaAmi1 were designed by fusion to its N-terminus two short antimicrobial peptides (AMPs). One AMP was selected by searching the genomes of Propionibacterium bacteriophages using bioinformatics tools, whereas the other AMP sequence was selected from the antimicrobial peptide databases. Both engineered variants exhibited improved lytic activity towards P. acnes and the enterococci species Enterococcus faecalis and Enterococcus faecium. The results of the present study suggest that PaAmi1 is a new antimicrobial agent and provide proof of concept that bacteriophage genomes are a rich source of AMP sequences that can be further exploited for designing novel or improved endolysins.

Structural and functional features of a broad-spectrum prophage-encoded enzybiotic from Enterococcus faecium

Multidrug-resistant (MDR) bacteria have become a growing threat to public health. The gram-positive Enterococcus faecium is classified by WHO as a high-priority pathogen among the global priority list of antibiotic-resistant bacteria. Peptidoglycan-degrading enzymes (PDEs), also known as enzybiotics, are useful bactericidal agents in the fight against resistant bacteria. In this work, a genome-based screening approach of the genome of E. faecium allowed the identification of a putative PDE gene with predictive amidase activity (EfAmi1; EC 3.5.1.28) in a prophage-integrated sequence. EfAmi1 is composed by two domains: a N-terminal Zn²⁺-dependent N-acetylmuramoyl-L-alanine amidase-2 (NALAA-2) domain and a C-terminal domain with unknown structure and function. The full-length gene of EfAmi1 was cloned and expressed as a 6xHis-tagged protein in E. coli. EfAmi1 was produced as a soluble protein, purified, and its lytic and antimicrobial activities were investigated using turbidity reduction and Kirby-Bauer disk-diffusion assays against clinically isolated bacterial pathogens. The crystal structure of the N-terminal amidase-2 domain was determined using X-ray crystallography at 1.97 Å resolution. It adopts a globular fold with several α-helices surrounding a central five-stranded β-sheet. Sequence comparison revealed a cluster of conserved amino acids that defines a putative binding site for a buried zinc ion. The results of the present study suggest that EfAmi1 displays high lytic and antimicrobial activity and may represent a promising new antimicrobial in the post-antibiotic era.

Endolysins of bacteriophages

Bacteriophage endolysins are a biologically active substances that play a specific role in the release of phage progeny by degrading the peptidoglycan of the host bacterium. In the light of antibiotic resistance, endolysins are considered as alternative therapeutic agents because of their exceptional ability to target bacterial cells. Aim summarization of the data on the biology, structure, mechanisms of action of bacteriophage endolysins, as well as on preparations based on them, which are at different stages of research. The results of studies of bacterial endolysins over the past 20 years were searched using the Internet resources PubMed, Web of Science, Scopus in English for the keywords: lysin, bacteriophages, holin, antibiotic resistance. The analysis of literature data showed that the structure of phage endolysins of Gram-positive and Gram-negative bacteria differs from each other and reflects differences in their architecture due to variation in the cell wall composition of these two major bacterial groups. Depending on the cleavable bond in peptidoglycan, endolysins can be divided into at least five different groups: glycosidases (two groups aminidases and muramidases), endopeptidases, specific amidogyrolases, and lytic transglycosylases. To date, endolysins effective against a number of pathogens have been studied, including Streptococcus pneumoniae, Streptococcus pyogenes, Streptococcus agalactiae, Staphylococcus aureus, Mycobacterium spp., Pseudomonas aeruginosa, etc. A number of studies have shown the therapeutic potential of endolysins in combating antibiotic-resistant infections.

Rapid Screening and Comparison of Chimeric Lysins for Antibacterial Activity against Staphylococcus aureus Strains

Chimeric lysins composed of various combinations of cell wall-lysing (enzymatic) and cell-wall-binding (CWB) domains of endolysins, autolysins, and bacteriocins have been developed as alternatives to or adjuvants of conventional antibiotics. The screening of multiple chimeric lysin candidates for activity via E. coli expression is not cost effective, and we previously reported on a simple cell-free expression system as an alternative. In this study, we sufficiently improved upon this cell-free expression system for use in screening activity via a turbidity reduction test, which is more appropriate than a colony reduction test when applied in multiple screening. Using the improved protocol, we screened and compared the antibacterial activity of chimeric lysin candidates and verified the relatively strong activity associated with the CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) domain of secretory antigen SsaA-like protein (ALS2). ALS2 expressed in E. coli showed two major bands, and the smaller one (subprotein) was shown to be expressed by an innate downstream promoter and start codon (ATG). The introduction of synonymous mutations in the promoter resulted in clearly reduced expression of the subprotein, whereas missense mutations in the start codon abolished antibacterial activity as well as subprotein production. Interestingly, most of the S. aureus strains responsible for bovine mastitis were susceptible to ALS2, but those from human and chicken were less susceptible. Thus, the simple and rapid screening method can be applied to select functional chimeric lysins and define mutations affecting antibacterial activity, and ALS2 may be useful in itself and as a lead molecule to control bovine mastitis.

A novel bacteriocin against multiple foodborne pathogens from Lacticaseibacillus rhamnosus isolated from juice ferments: ATF perfusion-based preparation of viable cells, characterization, antibacterial and antibiofilm activity

Foodborne pathogens and their biofilms pose a risk to human health through food chain. However, the bacteriocin resources combating this threat are still limited. Here, Lacticaseibacillus rhamnosus, one of the most used probiotics in food industry, was prepared on a large scale using alternating tangential flow (ATF) perfusion-based technology. Compared to the conventional fed-batch approach, ATF perfusion remarkably increased the viable cells of L. rhamnosus CLK 101 to 11.93 ± 0.14 log CFU/mL. Based on obtained viable cells, we purified and characterized a novel bacteriocin CLK_01 with a broad spectrum of activity against both Gram-positive and Gram-negative foodborne pathogens. LC-MS/MS analysis revealed that CLK_01 has a molecular mass of 701.49 Da and a hydrophobic amino acid composition of I-K-K-V-T-I. As a novel bacteriocin, CLK_01 showed high thermal stability and acid-base tolerance over 25-121 °C and pH 2-10. It significantly reduced cell viability of bacterial pathogens (p < 0.001), and strongly inhibited their biofilm formation. Scanning electron microscopy demonstrated deformation of pathogenic cells caused by CLK_01, leading to cytoplasmic content leakage and bacterial death. Summarily, we employed ATF perfusion to obtain viable L. rhamnosus, and presented that bacteriocin CLK_01 could serve as a promising biopreservative for controlling foodborne pathogenic bacteria and their biofilms.

Interrogation of the contribution of (endo)lysin domains to tune their bacteriolytic efficiency provides a novel clue to design superior antibacterials

Bacteriophage-derived endolysins and bacterial autolysins (hereinafter lysins) represent a completely new class of efficient antibacterials. They prevent the development of bacterial resistance and help protect commensal microbiota, producing cell wall lysis. Here we have investigated whether the acquisition of enzymatic active domains (EADs) and cell wall binding domains (CWBDs) of balancing efficiencies could be a way of tuning natural lysin activity. The concept was applied to produce a chimeric lysin of superior antibacterial capacity using the endolysin Skl and the major pneumococcal autolysin LytA. Combination of the Skl EAD and the cell wall choline-binding domain (CBD) of LytA in the chimera QSLA increased the bacterial killing by 2 logs or more compared to parental enzymes at an equal concentration and extended the substrate range to resistant and emergent pneumococci and other pathogens of the mitis group. Contrarily, QLAS, containing LytA EAD and Skl CBD, was inactive against all tested strains, although domain structures were preserved and hydrolysis of purified cell walls maintained in both chimeras. As a whole, our study provides a novel clue to design superior lysins to fight multidrug-resistant pathogens based on domain selection, and a powerful in-vivo active lysin (QSLA) with promising therapeutic perspectives.

Imbalance of peptidoglycan biosynthesis alters the cell surface charge of Listeria monocytogenes

The bacterial cell wall is composed of a thick layer of peptidoglycan and cell wall polymers, which are either embedded in the membrane or linked to the peptidoglycan backbone and referred to as lipoteichoic acid (LTA) and wall teichoic acid (WTA), respectively. Modifications of the peptidoglycan or WTA backbone can alter the susceptibility of the bacterial cell towards cationic antimicrobials and lysozyme. The human pathogen Listeria monocytogenes is intrinsically resistant towards lysozyme, mainly due to deacetylation and O-acetylation of the peptidoglycan backbone via PgdA and OatA. Recent studies identified additional factors, which contribute to the lysozyme resistance of this pathogen. One of these is the predicted ABC transporter, EslABC. An eslB mutant is hyper-sensitive towards lysozyme, likely due to the production of thinner and less O-acetylated peptidoglycan. Using a suppressor screen, we show here that suppression of eslB phenotypes could be achieved by enhancing peptidoglycan biosynthesis, reducing peptidoglycan hydrolysis or alterations in WTA biosynthesis and modification. The lack of EslB also leads to a higher negative surface charge, which likely stimulates the activity of peptidoglycan hydrolases and lysozyme. Based on our results, we hypothesize that the portion of cell surface exposed WTA is increased in the eslB mutant due to the thinner peptidoglycan layer and that latter one could be caused by an impairment in UDP-N-acetylglucosamine (UDP-GlcNAc) production or distribution.

One fold, many functions-M23 family of peptidoglycan hydrolases

Bacterial cell walls are the guards of cell integrity. They are composed of peptidoglycan that provides rigidity to sustain internal turgor and ensures isolation from the external environment. In addition, they harbor the enzymatic machinery to secure cell wall modulations needed throughout the bacterial lifespan. The main players in this process are peptidoglycan hydrolases, a large group of enzymes with diverse specificities and different mechanisms of action. They are commonly, but not exclusively, found in prokaryotes. Although in most cases, these enzymes share the same molecular function, namely peptidoglycan hydrolysis, they are leveraged to perform a variety of physiological roles. A well-investigated family of peptidoglycan hydrolases is M23 peptidases, which display a very conserved fold, but their spectrum of lytic action is broad and includes both Gram- positive and Gram- negative bacteria. In this review, we summarize the structural, biochemical, and functional studies concerning the M23 family of peptidases based on literature and complement this knowledge by performing large-scale analyses of available protein sequences. This review has led us to gain new insight into the role of surface charge in the activity of this group of enzymes. We present relevant conclusions drawn from the analysis of available structures and indicate the main structural features that play a crucial role in specificity determination and mechanisms of latency. Our work systematizes the knowledge of the M23 family enzymes in the context of their unique antimicrobial potential against drug-resistant pathogens and presents possibilities to modulate and engineer their features to develop perfect antibacterial weapons.

The Mechanism of Bacterial Resistance and Potential Bacteriostatic Strategies

Bacterial drug resistance is rapidly developing as one of the greatest threats to human health. Bacteria will adopt corresponding strategies to crack the inhibitory effect of antibiotics according to the antibacterial mechanism of antibiotics, involving the mutation of drug target, secreting hydrolase, and discharging antibiotics out of cells through an efflux pump, etc. In recent years, bacteria are found to constantly evolve new resistance mechanisms to antibiotics, including target protective protein, changes in cell morphology, and so on, endowing them with multiple defense systems against antibiotics, leading to the emergence of multi-drug resistant (MDR) bacteria and the unavailability of drugs in clinics. Correspondingly, researchers attempt to uncover the mystery of bacterial resistance to develop more convenient and effective antibacterial strategies. Although traditional antibiotics still play a significant role in the treatment of diseases caused by sensitive pathogenic bacteria, they gradually lose efficacy in the MDR bacteria. Therefore, highly effective antibacterial compounds, such as phage therapy and CRISPER-Cas precision therapy, are gaining an increasing amount of attention, and are considered to be the treatments with the moist potential with regard to resistance against MDR in the future. In this review, nine identified drug resistance mechanisms are summarized, which enhance the retention rate of bacteria under the action of antibiotics and promote the distribution of drug-resistant bacteria (DRB) in the population. Afterwards, three kinds of potential antibacterial methods are introduced, in which new antibacterial compounds exhibit broad application prospects with different action mechanisms, the phage therapy has been successfully applied to infectious diseases caused by super bacteria, and the CRISPER-Cas precision therapy as a new technology can edit drug-resistant genes in pathogenic bacteria at the gene level, with high accuracy and flexibility. These antibacterial methods will provide more options for clinical treatment, and will greatly alleviate the current drug-resistant crisis.

Electrostatic Interaction with the Bacterial Cell Envelope Tunes the Lytic Activity of Two Novel Peptidoglycan Hydrolases

Peptidoglycan (PG) hydrolases, due to their crucial role in the metabolism of the bacterial cell wall (CW), are increasingly being considered suitable targets for therapies, and a potent alternative to conventional antibiotics. In the light of contradictory data reported, detailed mechanism of regulation of enzymes activity based on electrostatic interactions between hydrolase molecule and bacterial CW surface remains unknown. Here, we report a comprehensive study on this phenomenon using as a model two novel PG hydrolases, SpM23_A, and SpM23_B, which although share the same bacterial host, similarities in sequence conservation, domain architecture, and structure, display surprisingly distinct net charges (in 2D electrophoresis, pI 6.8, and pI 9.7, respectively). We demonstrate a strong correlation between hydrolases surface net charge and the enzymes activity by modulating the charge of both, enzyme molecule and bacterial cell surface. Teichoic acids, anionic polymers present in the bacterial CW, are shown to be involved in the mechanism of enzymes activity regulation by the electrostatics-based interplay between charged bacterial envelope and PG hydrolases. These data serve as a hint for the future development of chimeric PG hydrolases of desired antimicrobial specificity. IMPORTANCE This study shows direct relationship between the surface charge of two recently described enzymes, SpM23_A and SpM23_B, and bacterial cell walls. We demonstrate that by (i) surface charge probing of bacterial strains collection, (ii) reduction of the net charge of the positively charged enzyme, and (iii) altering the net charge of the bacterial surface by modifying the content and composition of teichoic acids. In all cases, we observed that lytic activity and binding strength of SpM23 enzymes, are regulated by electrostatic interactions with the bacterial cell envelope and that this interaction contributes to the determination of the spectrum of susceptible bacterial species. Moreover, we revealed the regulatory role of charged cell wall components, namely, teichoic and lipoteichoic acids, over the SpM23 enzymes. We believe that our findings make an important contribution to understand the means of hydrolases activity regulation in the complex environment of the bacterial cell wall.

Bacteriostatic effects of phage F23s1 and its endolysin on Vibrio parahaemolyticus

Vibrio parahaemolyticus is a common foodborne pathogenic bacterium and drug-resistant strains are now widespread. Phages led by drug-resistant V. parahaemolyticus strains are promising means to decrease the pressure on public health. We isolated a V. parahaemolyticus-specific bacteriophage F23s1 that was active at wide ranges of temperature (30-60°C) and pH (4-10). Phage F23s1 exhibited a specific host range; in that, only 13 of the 23 V. parahaemolyticus strains were lysed. F23s1 effectively inhibited the growth of V. parahaemolyticus strain F23 in shrimp at 25°C within 12 h at a multiplicity of infection of 1000. We sequenced the genome of phage F23s1 which comprised a 76,648-bp DNA with 105 open reading frames (ORFs) and identified an endolysin gene ORF52 that was then cloned and successfully expressed in Escherichia coli. The recombinant ORF52 protein significantly decreased OD_600 nm of V. parahaemolyticus F23 from 0.978 to 0.249 when used at 20 µmol/L within 60 min. The endolysin also showed lytic activity against a panel of 23 drug-resistant V. parahaemolyticus and 12 Salmonella strains with a higher lytic ability for V. parahaemolyticus. The phage F23s1 and its endolysin will be useful for preventing and controlling V. parahaemolyticus in food safety.

Substantiation of propitious "Enzybiotic" from two novel bacteriophages isolated from a wastewater treatment plant in Qatar

Lysin of bacteriophages isolated from a particular ecosystem could be inducted as a bio-controlling tool against the inhabiting pathogenic bacterial strains. Our study aims at both experimental and computational characterization of the identical lysin gene product inherent in the genomes of two novel Myoviridae bacteriophages, Escherichia Phage C600M2 (GenBank accession number OK040807, Protein ID: UCJ01465) and Escherichia Phage CL1 (GenBank Genome accession number OK040806.1, Protein ID: UCJ01321) isolated from wastewater collected from the main water treatment plant in Qatar. The lysin protein, evinced to be a globular N-acetyl-muramidase with intrinsic “cd00737: endolysin_autolysin” domain, was further expressed and purified to be experimentally validated by turbidimetric assay for its utility as an anti-bacterial agent. Comprehensive computational analysis revealed that the scrutinized lysin protein shared 85–98% sequence identity with 61 bacteriophages, all native to wastewater allied environments. Despite varied Host Recognition Components encoded in their genomes, the similitude of lysins, suggests its apparent significance in host–pathogen interactions endemic to wastewater environment. The present study substantiates the identical lysin from Escherichia Phage C600M2 and Escherichia Phage CL1 as propitious “enzybiotic”, a hybrid term to describe enzymes analogous to anti-biotics to combat antibiotic-resistant bacteria by in silico analysis and subsequent experimental validation.

Potential Role of the Host-Derived Cell-Wall Binding Domain of Endolysin CD16/50L as a Molecular Anchor in Preservation of Uninfected Clostridioides difficile for New Rounds of Phage Infection

Endolysin is a phage-encoded cell-wall hydrolase which degrades the peptidoglycan layer of the bacterial cell wall. The enzyme is often expressed at the late stage of the phage lytic cycle and is required for progeny escape. Endolysins of bacteriophage that infect Gram-positive bacteria often comprises two domains: a peptidoglycan hydrolase and a cell-wall binding domain (CBD). Although the catalytic domain of endolysin is relatively well-studied, the precise role of CBD is ambiguous and remains controversial. Here, we focus on the function of endolysin CBD from a recently isolated Clostridioides difficile phage. We found that the CBD is not required for lytic activity, which is strongly prevented by the surface layer of C. difficile. Intriguingly, hidden Markov model analysis suggested that the endolysin CBD is likely derived from the CWB2 motif of C. difficile cell-wall proteins but possesses a higher binding affinity to bacterial cell-wall polysaccharides. Moreover, the CBD forms a homodimer, formation of which is necessary for interaction with the surface saccharides. Importantly, endolysin diffusion and sequential cytolytic assays showed that CBD of endolysin is required for the enzyme to be anchored to post-lytic cell-wall remnants, suggesting its physiological roles in limiting diffusion of the enzyme, preserving neighboring host cells, and thereby enabling the phage progeny to initiate new rounds of infection. Taken together, this study provides an insight into regulation of endolysin through CBD and can potentially be applied for endolysin treatment against C. difficile infection. IMPORTANCE Endolysin is a peptidoglycan hydrolase encoded in a phage genome. The enzyme is attractive due to its potential use as antibacterial treatment. To utilize endolysin for the therapeutic propose, understanding of the fundamental role of endolysin becomes important. Here, we investigate the function of cell-wall binding domain (CBD) of an endolysin from a C. difficile phage. The domain is homologous to a cell-wall associating module of bacterial cell-wall proteins, likely acquired during phage-host coevolution. The interaction of CBD to bacterial cell walls reduces enzyme diffusion and thereby limits cell lysis of the neighboring bacteria. Our findings indicate that the endolysin is trapped to the cell-wall residuals through CBD and might serve as an advantage for phage replication. Thus, employing a CBD-less endolysin might be a feasible strategy for using endolysin for the treatment of C. difficile infection.

Bacteriophage and endolysin engineering for biocontrol of food pathogens/pathogens in the food: recent advances and future trends

Despite advances in modern technologies, various foodborne outbreaks have continuously threatened the food safety. The overuse of and abuse/misuse of antibiotics have escalated this threat due to the prevalence of multidrug-resistant (MDR) pathogens. Therefore, the development of new methodologies for controlling microbial contamination is extremely important to ensure the food safety. As an alternative to antibiotics, bacteriophages(phages) and derived endolysins have been proposed as novel, effective, and safe antimicrobial agents and applied for the prevention and/or eradication of bacterial contaminants even in foods and food processing facilities. In this review, we describe recent genetic and protein engineering tools for phages and endolysins. The major aim of engineering is to overcome limitations such as a narrow host range, low antimicrobial activity, and low stability of phages and endolysins. Phage engineering also aims to deter the emergence of phage resistance. In the case of endolysin engineering, enhanced antibacterial ability against Gram-negative and Gram-positive bacteria is another important goal. Here, we summarize the successful studies of phages and endolysins treatment in different types of food. Moreover, this review highlights the recent advances in engineering techniques for phages and endolysins, discusses existing challenges, and suggests technical opportunities for further development, especially in terms of antimicrobial agents in the food industry.

Monomodular Pseudomonas aeruginosa phage JG004 lysozyme (Pae87) contains a bacterial surface-active antimicrobial peptide-like region and a possible substrate-binding subdomain

The structure of the monomodular Pseudomonas aeruginosa bacteriophage JG004 lysin Pae87 is presented and investigated in relation to repurposing its function as an antimicrobial agent. The structure with its peptidoglycan ligand revealed a possible cell-wall-binding region. A C-terminal antimicrobial peptide-like region is shown to be important for disrupting the bacterial cell wall.

Phage lysins are a source of novel antimicrobials to tackle the bacterial antibiotic-resistance crisis. The engineering of phage lysins is being explored as a game-changing technological strategy to introduce a more precise approach in the way in which antimicrobial therapy is applied. Such engineering efforts will benefit from a better understanding of lysin structure and function. In this work, the antimicrobial activity of the endolysin from Pseudomonas aeruginosa phage JG004, termed Pae87, has been characterized. This lysin had previously been identified as an antimicrobial agent candidate that is able to interact with the Gram-negative surface and disrupt it. Further evidence is provided here based on a structural and biochemical study. A high-resolution crystal structure of Pae87 complexed with a peptidoglycan fragment showed a separate substrate-binding region within the catalytic domain, 18 Å away from the catalytic site and located on the opposite side of the lysin molecule. This substrate-binding region was conserved among phylogenetically related lysins lacking an additional cell-wall-binding domain, but not among those containing such a module. Two glutamic acids were identified to be relevant for the peptidoglycan-degradation activity, although the antimicrobial activity of Pae87 was seemingly unrelated. In contrast, an antimicrobial peptide-like region within the Pae87 C-terminus, named P87, was found to be able to actively disturb the outer membrane and display antibacterial activity by itself. Therefore, an antimicrobial mechanism for Pae87 is proposed in which the P87 peptide plays the role of binding to the outer membrane and disrupting the cell-wall function, either with or without the participation of the catalytic activity of Pae87.

Bacteriophage Lytic Enzyme P9ly as an Alternative Antibacterial Agent Against Antibiotic-Resistant Shigella dysenteriae and Staphylococcus aureus

Developing new strategies to replace or supplement antibiotics to combat bacterial infection is a pressing task in the field of microbiological research. In this study, we report a lytic enzyme named P9ly deriving from the bacteriophage PSD9 that could infect multidrug-resistant Shigella. This enzyme was identified through whole-genome sequencing of PSD9. The results show that P9ly contains a conserved T4-like_lys domain and belongs to the phage lysozyme family. Recombinant P9ly obtained from protein purification presented biological activity and could digest bacterial cell walls (CW), resulting in the destruction of cell structure and leakage of intracellular components. Furthermore, P9ly exhibited bacteriolytic and bactericidal activity on different strains, especially multidrug-resistant Gram-negative Shigella dysenteriae and Gram-positive Staphylococcus aureus. Additionally, combined use of P9ly with ceftriaxone sodium (CRO) could decrease necessary dose of the antibiotic used and improve the antibacterial effect. In summary, under the current backdrop of extensive antibiotic usage and the continuous emergence of bacterial resistance, this study provides an insight into developing bacteriophage-based antibacterial agents against both Gram-negative and Gram-positive pathogens.

In-situ and Real-Time Monitoring of the Interaction Between Lysins and Staphylococcus aureus Biofilm by Surface Plasmon Resonance

Staphylococcus aureus can produce a multilayered biofilm embedded in extracellular polymeric matrix. This biofilm is difficult to remove, insensitive to antibiotics, easy to develop drug-resistant strains and causes enormous problems to environments and health. Phage lysin which commonly consists of a catalytic domain (CD) and a cell-wall binding domain (CBD) is a powerful weapon against bacterial biofilm. However, the real-time interaction between lysin and S. aureus biofilm is still not fully understood. In this study, we monitored the interactions of three lysins (ClyF, ClyC, PlySs2) against culture-on-chip S. aureus biofilm, in real-time, based on surface plasmon resonance (SPR). A typical SPR response curve showed that the lysins bound to the biofilm rapidly and the biofilm destruction started at a longer time. By using 1:1 binding model analysis, affinity constants (K_D) for ClyF, ClyC, and PlySs2 were found to be 3.18 ± 0.127 μM, 1.12 ± 0.026 μM, and 15.5 ± 0.514 μM, respectively. The fact that ClyF and PlySs2 shared the same CBD but showed different affinity to S. aureus biofilm suggested that, not only CBD, but also CD affects the binding activity of the entire lysin. The SPR platform can be applied to improve our understanding on the complex interactions between lysins and bacterial biofilm including association (adsorption) and disassociation (destruction).

Endolysin, a Promising Solution against Antimicrobial Resistance

Antimicrobial resistance (AMR) is a global crisis for human public health which threatens the effective prevention and control of ever-increasing infectious diseases. The advent of pandrug-resistant bacteria makes most, if not all, available antibiotics invalid. Meanwhile, the pipeline of novel antibiotics development stagnates, which prompts scientists and pharmacists to develop unconventional antimicrobials. Bacteriophage-derived endolysins are cell wall hydrolases which could hydrolyze the peptidoglycan layer from within and outside of bacterial pathogens. With high specificity, rapid action, high efficiency, and low risk of resistance development, endolysins are believed to be among the best alternative therapeutic agents to treat multidrug resistant (MDR) bacteria. As of now, endolysins have been applied to diverse aspects. In this review, we comprehensively introduce the structures and activities of endolysins and summarize the latest application progress of recombinant endolysins in the fields of medical treatment, pathogen diagnosis, food safety, and agriculture.

Improved antimicrobial spectrum of the N-acetylmuramoyl-L-alanine amidase from Latilactobacillus sakei upon LysM domain deletion

The gene encoding N-acetylmuramoyl-L-alanine amidase in Latilactobacillus sakei isolated from a fermented meat product was cloned in two forms: its complete sequence (AmiC) and a truncated sequence without one of its anchoring LysM domains (AmiLysM4). The objective of this work was to evaluate the effect of LysM domain deletion on antibacterial activity as well the biochemical characterization of each recombinant protein. AmiC and AmiLysM4 were expressed in Escherichia coli BL21. Using a zymography method, two bands with lytic activity were observed, which were confirmed by LC-MS/MS analysis, with molecular masses of 71 kDa (AmiC) and 66 kDa (AmiLysM4). The recombinant proteins were active against Listeria innocua and Staphylococcus aureus strains. The inhibitory spectrum of AmiLysM4 was broader than AmiC as it showed inhibition of Leuconostoc mesenteroides and Weissella viridescens, both microorganisms associated with food decomposition. Optimal temperature and pH values were determined for both proteins using L-alanine-p-nitroanilide hydrochloride as a substrate for N-acetylmuramoyl-L-alanine amidase activity. Both proteins showed similar maximum activity values for pH (8) and temperature (50 °C). Furthermore, structural predictions did not show differences for the catalytic region, but differences were found for the region called 2dom-AmiLysM4, which includes 4 of the 5 LysM domains. Therefore, modification of the LysM domain offers new tools for the development of novel food biopreservatives.

Two New M23 Peptidoglycan Hydrolases With Distinct Net Charge

Bacterial peptidoglycan hydrolases play an essential role in cell wall metabolism during bacterial growth, division, and elongation (autolysins) or in the elimination of closely related species from the same ecological niche (bacteriocins). Most studies concerning the peptidoglycan hydrolases present in Gram-positive bacteria have focused on clinically relevant Staphylococcus aureus or the model organism Bacillus subtilis, while knowledge relating to other species remains limited. Here, we report two new peptidoglycan hydrolases from the M23 family of metallopeptidases derived from the same staphylococcal species, Staphylococcus pettenkoferi. They share modular architecture, significant sequence identity (60%), catalytic and binding residue conservation, and similar modes of activation, but differ in gene distribution, putative biological role, and, strikingly, in their isoelectric points (pIs). One of the peptides has a high pI, similar to that reported for all M23 peptidases evaluated to date, whereas the other displays a low pI, a unique feature among M23 peptidases. Consequently, we named them SpM23_B (Staphylococcus pettenkoferi M23 "Basic") and SpM23_A (Staphylococcus pettenkoferi M23 "Acidic"). Using genetic and biochemical approaches, we have characterized these two novel lytic enzymes, both in vitro and in their physiological context. Our study presents a detailed characterization of two novel and clearly distinct peptidoglycan hydrolases to understand their role in bacterial physiology.

Bacteriophage endolysins against gram-positive bacteria, an overview on the clinical development and recent advances on the delivery and formulation strategies

Facing the increasing threat of multi-drug antimicrobial resistance (AMR), humans strive to search for antibiotic drug candidates and antibacterial alternatives from all possible places, from soils in remote areas to deep in the sea. In this "gold rush for antibacterials," researchers turn to the natural enemy of bacterial cells, bacteriophage (phages), and find them a rich source of weapons for AMR bacteria. Endolysins (lysins), the enzymes phages use to break the bacterial cells from within, have been shown to be highly selective and efficient in killing their target bacteria from outside while maintaining a low occurrence of bacterial resistance. In this review, we start with the structures and mechanisms of action of lysins against Gram-positive (GM+) bacteria. The developmental history of lysins is also outlined. Then, we detail the latest preclinical and clinical research on their safety and efficacy against GM+ bacteria, focusing on the formulation strategies of these enzymes. Finally, the challenges and potential hurdles are discussed. Notwithstanding these limitations, the trends in development indicate that the first, approved lysin drugs will be available soon in the near future. Overall, this review presents a timely summary of the current progress on lysins as antibacterial enzymes for AMR GM+ bacteria, and provides a guidebook for biomaterial researchers who are dedicating themselves to the battle against bacterial infections.

Sequence-Function Relationships in Phage-Encoded Bacterial Cell Wall Lytic Enzymes and Their Implications for Phage-Derived Product Design

Phage (endo)lysins are thought to be a viable alternative to usual antibiotic chemotherapy to fight resistant bacterial infections. However, a comprehensive view of lysins' structure and properties regarding their function, with an applied focus, is somewhat lacking. Current literature suggests that specific features typical of lysins from phages infecting Gram-negative bacteria (G-) (higher net charge and amphipathic helices) are responsible for improved interaction with the G- envelope. Such antimicrobial peptide (AMP)-like elements are also of interest for antimicrobial molecule design. Thus, this study aims to provide an updated view on the primary structural landscape of phage lysins to clarify the evolutionary importance of several sequence-predicted properties, particularly for the interaction with the G- surface. A database of 2,182 lysin sequences was compiled, containing relevant information such as domain architectures, data on the phages' host bacteria, and sequence-predicted physicochemical properties. Based on such classifiers, an investigation of the differential appearance of certain features was conducted. This analysis revealed different lysin architectural variants that are preferably found in phages infecting certain bacterial hosts. In particular, some physicochemical properties (higher net charge, hydrophobicity, hydrophobic moment, and aliphatic index) were associated with G- phage lysins, appearing specifically at their C-terminal end. Information on the remarkable genetic specialization of lysins regarding the features of the bacterial hosts is provided, specifically supporting the nowadays-common hypothesis that lysins from G- usually contain AMP-like regions. IMPORTANCE Phage-encoded lytic enzymes, also called lysins, are one of the most promising alternatives to common antibiotics. The potential of lysins as novel antimicrobials to tackle antibiotic-resistant bacteria not only arises from features such as a lower chance to provoke resistance but also from their versatility as synthetic biology parts. Functional modules derived from lysins are currently being used for the design of novel antimicrobials with desired properties. This study provides a view of the lysin diversity landscape by examining a set of phage lysin genes. We have uncovered the fundamental differences between the lysins from phages that infect bacteria with different superficial architectures and, thus, the reach of their specialization regarding cell wall structures. These results provide clarity and evidence to sustain some of the common hypotheses in current literature, as well as making available an updated and characterized database of lysins sequences for further developments.

Characterization of two newly isolated bacteriophages PW2 and PW4 and derived endolysins with lysis activity against Bacillus cereus group strains

This study characterized two novel Siphoviridae phages, PW2 and PW4, that can infect 52% and 44% of the tested Bacillus cereus group isolates and display relatively high activity against four cereulide-producing isolates belonging to B. weihenstephanensis and B. paranthracis. The genome sequences of PW2 and PW4 are similar to six known phages infecting B. cereus group isolates, which can be classified into two conserved groups, with the PW2 genome harboring conserved coding sequences (CDSs) from both groups. Two phage-derived endolysins, LysPW2 and LysPW4, which are predicted to encode N-acetylmuramoyl-L-alanine amidase, and their enzymatically active domains (EADs), LysPW2-EAD and LysPW4-EAD, were heterologously expressed. Both LysPW2 and LysPW4, especially the former, show a much wider host range than the phages, albeit still limited to the B. cereus group for the tested bacteria. The optimal temperature and pH for LysPW2 ability is 37 °C and pH 8.0 and for LysPW4 is 50 °C and pH 9.0. Neither LysPW2-EAD nor LysPW4-EAD show any lytic activity against vegetative cells of the tested B. cereus group isolates but can inhibit germination in 66.3% and 65.7% of spores, respectively. In addition, both LysPW2-EAD and LysPW4-EAD exhibit spore-binding capabilities.

Cloning and expression analysis of fused holin-endolysin from RL bacteriophage; Exhibits broad activity against multi drug resistant pathogens

Antibiotic resistance has become a major risk to community health over last few years because of antibiotics overuse around the globe and lack of new antibiotics development. Phages and their lytic enzymes are considered as an effective alternative of antibiotics to control drug resistant bacterial pathogens. Endolysins prove to be a promising class of antibacterials due to their specificity and less chances of resistance development in bacterial pathogens. Though large number of endolysins has been reported against gram positive bacteria, very few reported against gram negative bacteria due to the presence of outer membrane, which acts as physical barrier against endolysin attack to peptidoglycan. In the current study, we have expressed endolysin (RL_Lys) and holin fused at the N terminus of endolysin (RL_Hlys) from RL phage infecting multi drug resistant (MDR) Pseudomonas aeruginosa. Both endolysin variants were found active against wide range of MDR strains P. aeruginosa, Klebsella pneumonia, Salmonella Sp. and Methicillin Resistant Staphylococcus aureus (MRSA). Broth reduction assay showed that RL_Hlys is more active than RL_Lys due to presence of holin, which assist the endolysin access towards cell wall. The protein ligand docking and molecular dynamic simulation results showed that C- terminus region of endolysin play vital role in cell wall binding and even in the absence of holin, hydrolyze a broad range of gram negative bacterial pathogens. The significant activity of RL-Lys and RL_Hlys against a broad range of MDR gram negative and positive bacterial pathogens makes them good candidates for antibiotic alternatives.

Characterization of an Endolysin Targeting Clostridioides difficile That Affects Spore Outgrowth

Clostridioides difficile is a spore-forming enteric pathogen causing life-threatening diarrhoea and colitis. Microbial disruption caused by antibiotics has been linked with susceptibility to, and transmission and relapse of, C. difficile infection. Therefore, there is an urgent need for novel therapeutics that are effective in preventing C. difficile growth, spore germination, and outgrowth. In recent years bacteriophage-derived endolysins and their derivatives show promise as a novel class of antibacterial agents. In this study, we recombinantly expressed and characterized a cell wall hydrolase (CWH) lysin from C. difficile phage, phiMMP01. The full-length CWH displayed lytic activity against selected C. difficile strains. However, removing the N-terminal cell wall binding domain, creating CWH_351—656, resulted in increased and/or an expanded lytic spectrum of activity. C. difficile specificity was retained versus commensal clostridia and other bacterial species. As expected, the putative cell wall binding domain, CWH_1—350, was completely inactive. We also observe the effect of CWH_351—656 on preventing C. difficile spore outgrowth. Our results suggest that CWH_351—656 has therapeutic potential as an antimicrobial agent against C. difficile infection.

The multidomain architecture of a bacteriophage endolysin enables intramolecular synergism and regulation of bacterial lysis

Endolysins are peptidoglycan hydrolases produced at the end of the bacteriophage (phage) replication cycle to lyse the host cell. Endolysins in Gram-positive phages come in a variety of multimodular forms that combine different catalytic and cell wall binding domains. However, the reason why phages adopt endolysins with such complex multidomain architecture is not well understood. In this study, we used the Streptococcus dysgalactiae phage endolysin PlySK1249 as a model to investigate the role of multidomain architecture in phage-induced bacterial lysis and lysis regulation. PlySK1249 consists of an amidase (Ami) domain that lyses bacterial cells, a nonbacteriolytic endopeptidase (CHAP) domain that acts as a dechaining enzyme, and a central LysM cell wall binding domain. We observed that the Ami and CHAP domains synergized for peptidoglycan digestion and bacteriolysis in the native enzyme or when expressed individually and reunified. The CHAP endopeptidase resolved complex polymers of stem-peptides to dimers and helped the Ami domain to digest peptidoglycan to completion. We also found that PlySK1249 was subject to proteolytic cleavage by host cell wall proteases both in vitro and after phage induction. Cleavage disconnected the different domains by hydrolyzing their linker regions, thus hindering their bacteriolytic cooperation and possibly modulating the lytic activity of the enzyme. PlySK1249 cleavage by cell-wall-associated proteases may represent another example of phage adaptation toward the use of existing bacterial regulation mechanism for their own advantage. In addition, understanding more thoroughly the multidomain interplay of PlySK1249 broadens our knowledge on the ideal architecture of therapeutic antibacterial endolysins.

High avidity drives the interaction between the streptococcal C1 phage endolysin, PlyC, with the cell surface carbohydrates of Group A Streptococcus

Endolysin enzymes from bacteriophage cause bacterial lysis by degrading the peptidoglycan cell wall. The streptococcal C1 phage endolysin PlyC, is the most potent endolysin described to date and can rapidly lyse group A, C, and E streptococci. PlyC is known to bind the Group A streptococcal cell wall, but the specific molecular target or the binding site within PlyC remain uncharacterized. Here we report for the first time, that the polyrhamnose backbone of the Group A streptococcal cell wall is the binding target of PlyC. We have also characterized the putative rhamnose binding groove of PlyC and found four key residues that were critical to either the folding or the cell wall binding action of PlyC. Based on our results, we suggest that the interaction between PlyC and the cell wall may not be a high-affinity interaction as previously proposed, but rather a high avidity one, allowing for PlyC's remarkable lytic activity. Resistance to our current antibiotics is reaching crisis levels and there is an urgent need to develop the antibacterial agents with new modes of action. A detailed understanding of this potent endolysin may facilitate future developments of PlyC as a tool against the rise of antibiotic resistance.

Lateral flow assay of methicillin-resistant Staphylococcus aureus using bacteriophage cellular wall-binding domain as recognition agent

As one of the most common and noticeable superbugs, methicillin-resistant Staphylococcus aureus (MRSA) has long been a major threat to public health. To meet the demand for effective diagnosis of MRSA-induced infection, it is urgent to establish rapid assay method for this type of pathogen. In this study, an aqueous soluble cellular wall-binding domain (CWBD) protein from bacteriophage P108 was obtained with a recombinant expression technique. It can act as a wide-spectrum binding agent for all MRSA strains and exclude the interference from methicillin-susceptible strains of Staphylococcus aureus and other species of bacteria. To establish a lateral flow assay (LFA) method for MRSA, CWBD-coupled time-resolved fluorescent microspheres (FMs) were used as signal probes for tracing MRSA, and a nitrocellulose membrane immobilized with porcine IgG was used to capture MRSA. With the LFA based on sandwich format, MRSA can be assayed within 10 min with a broad linear range of 6.6 × 10²-6.6 × 10⁷ CFU/mL. Its application potential has been demonstrated by assaying different types of bacteria-contaminated real samples. The results suggest that the LFA strip using recombinant CWBD as the recognition agent provides a rapid, portable, cost-effective approach for point-of-care testing of MRSA.

Electrostatic-Mediated Affinity Tuning of Lysostaphin Accelerates Bacterial Lysis Kinetics and Enhances In Vivo Efficacy

Drug-resistant bacterial pathogens are a serious threat to global health, and antibacterial lysins are at the forefront of innovative treatments for these life-threatening infections. While lysins' general mechanism of action is well understood, the design principles that might enable engineering of performance-enhanced variants are still being formulated. Here, we report a detailed analysis of molecular determinants underlying the in vivo efficacy of lysostaphin, a canonical anti-MRSA (methicillin-resistant Staphylococcus aureus) lysin. Systematic analysis of bacterial binding, growth inhibition, lysis kinetics, and in vivo therapeutic efficacy revealed that binding affinity, and not inherent catalytic firepower, is the dominant driver of lysostaphin efficacy. This insight enabled electrostatic affinity tuning of lysostaphin to produce a single point mutant that manifested dramatically enhanced processivity and lysis kinetics and trended toward improved in vivo efficacy. More generally, these studies provide important insights into the complex relationships between lysin electrostatics, bacterial targeting, cell lysis efficiency, and in vivo efficacy. The lessons learned may enable engineering of other high-performance antibacterial biocatalysts.

Fungal GH25 muramidases: New family members with applications in animal nutrition and a crystal structure at 0.78Å resolution

Muramidases/lysozymes hydrolyse the peptidoglycan component of the bacterial cell wall. They are found in many of the glycoside hydrolase (GH) families. Family GH25 contains muramidases/lysozymes, known as CH type lysozymes, as they were initially discovered in the Chalaropsis species of fungus. The characterized enzymes from GH25 exhibit both β-1,4-N-acetyl- and β-1,4-N,6-O-diacetylmuramidase activities, cleaving the β-1,4-glycosidic bond between N-acetylmuramic acid (NAM) and N-acetylglucosamine (NAG) moieties in the carbohydrate backbone of bacterial peptidoglycan. Here, a set of fungal GH25 muramidases were identified from a sequence search, cloned and expressed and screened for their ability to digest bacterial peptidoglycan, to be used in a commercial application in chicken feed. The screen identified the enzyme from Acremonium alcalophilum JCM 736 as a suitable candidate for this purpose and its relevant biochemical and biophysical and properties are described. We report the crystal structure of the A. alcalophilum enzyme at atomic, 0.78 Å resolution, together with that of its homologue from Trichobolus zukalii at 1.4 Å, and compare these with the structures of homologues. GH25 enzymes offer a new solution in animal feed applications such as for processing bacterial debris in the animal gut.

Simultaneous Control of Staphylococcus aureus and Bacillus cereus Using a Hybrid Endolysin LysB4EAD-LysSA11

Bacteriophage endolysins have attracted attention as promising alternatives to antibiotics, and their modular structure facilitates endolysin engineering to develop novel endolysins with enhanced versatility. Here, we constructed hybrid proteins consisting of two different endolysins for simultaneous control of two critical foodborne pathogens, Staphylococcus aureus and Bacillus cereus. The full-length or enzymatically active domain (EAD) of LysB4, an endolysin from the B. cereus-infecting phage B4, was fused to LysSA11, an endolysin of the S. aureus-infecting phage SA11, via a helical linker in both orientations. The hybrid proteins maintained the lytic activity of their parental endolysins against both S. aureus and B. cereus, but they showed an extended antimicrobial spectrum. Among them, the EAD of LysB4 fused with LysSA11 (LysB4EAD-LyaSA11) showed significantly increased thermal stability compared to its parental endolysins. LysB4EAD-LysSA11 exhibited high lytic activity at pH 8.0–9.0 against S. aureus and at pH 5.0–10.0 against B. cereus, but the lytic activity of the protein decreased in the presence of NaCl. In boiled rice, treatment with 3.0 µM of LysB4EAD-LysSA11 reduced the number of S. aureus and B. cereus to undetectable levels within 2 h and also showed superior antimicrobial activity to LyB4EAD and LysSA11 in combination. These results suggest that LysB4EAD-LysSA11 could be a potent antimicrobial agent for simultaneous control of S. aureus and B. cereus.

Design, Overproduction and Purification of the Chimeric Phage Lysin MLTphg Fighting against Staphylococcus aureus

With the increasing spread of multidrug-resistant bacterial pathogens, it is of great importance to develop alternatives to conventional antibiotics. Here, we report the generation of a chimeric phage lysin, MLTphg, which was assembled by joining the lysins derived from Meiothermus bacteriophage MMP7 and Thermus bacteriophage TSP4 with a flexible linker via chimeolysin engineering. As a potential antimicrobial agent, MLTphg can be obtained by overproduction in Escherichia coli BL21(DE3) cells and the following Ni-affinity chromatography. Finally, we recovered about 40 ± 1.9 mg of MLTphg from 1 L of the host E. coli BL21(DE3) culture. The purified MLTphg showed peak activity against Staphylococcus aureus ATCC6538 between 35 and 40 °C, and maintained approximately 44.5 ± 2.1% activity at room temperature (25 °C). Moreover, as a produced chimera, it exhibited considerably improved bactericidal activity against Staphylococcus aureus (2.9 ± 0.1 log10 reduction was observed upon 40 nM MLTphg treatment at 37 °C for 30 min) and also a group of antibiotic-resistant bacteria compared to its parental lysins, TSPphg and MMPphg. In the current age of growing antibiotic resistance, our results provide an engineering basis for developing phage lysins as novel antimicrobial agents and shed light on bacteriophage-based strategies to tackle bacterial infections.