Chimeric phage lysins act synergistically with lysostaphin to kill mastitis-causing Staphylococcus aureus in murine mammary glands

Structural Basis for the Essential Role of Ca2+ in the Lytic Activity of Staphylococcus aureus PlyGRCS Endolysin Targeting Methicillin-Resistant Staphylococcus aureus

Staphylococcus aureus causes a wide range of infections, from mild skin conditions to severe, life-threatening diseases. Bacteriophage endolysins exhibit a selective capacity to degrade the peptidoglycan layer of Gram-positive bacteria, making promising biotherapeutic agents against antibiotic-resistant infections. PlyGRCS, a specific endolysin derived from S. aureus, comprises a catalytic CHAP domain and a cell-wall binding SH3_5 domain connected by a linker. Ca2+ ions are essential for the CHAP domain's catalytic function. The crystal structure of PlyGRCS, determined in the absence of Ca2+ and refined to a resolution of 1.67 Å, revealed significant conformational changes in the Ca2+ binding site. Antimicrobial assays with Ca2+-deficient PlyGRCS and mutants targeting key residues in the catalytic and Ca2+ binding regions highlighted the importance of specific functional residues for lytic activity against methicillin-resistant Staphylococcus aureus (MRSA). These structural and microbial studies provide valuable insights into the critical residues contributing to PlyGRCS's bacteriolytic efficacy against MRSA.

The Synergistic and Chimeric Mechanism of Bacteriophage Endolysins: Opportunities for Application in Biotherapeutics, Food, and Health Sectors

A major growing concern in the human and animal health sector is the emergence of antibiotic-resistant pathogenic bacteria due to the indiscriminate use of antibiotics. The exogenous application of bacteriophage endolysins causes abrupt lysis of the bacterial cell wall, which computes them as alternatives to antibiotics. Although naturally occurring endolysins may display limitations in solubility, lytic activity, and narrow lytic spectrum, novel strategies like developing chimeric endolysins and using endolysins in synergism with other antimicrobial agents are required to improve the lytic activity of natural endolysins. The modular structure of endolysins led to the development of novel chimeric endolysins via shuffling enzymatic and cell wall binding domains of different endolysins, using endolysins in a synergistic approach, and their applications in various in vitro and in vivo experiments and different applicable areas. This article aims to review the role of chimeric endolysins and their use in synergistic mode with other biofilm-reducing agents to control biofilm formation and deteriorating pre-formed biofilms in food, dairy, and medical industries. Promoting further development of phage technology and innovation in antibiotic therapy can achieve long-term sustainable development and economic returns.

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.

Endolysin NC5 improves early cloxacillin treatment in a mouse model of Streptococcus uberis mastitis

Streptococcus uberis frequently causes bovine mastitis, an infectious udder disease with significant economic implications for dairy cows. Conventional antibiotics, such as cloxacillin, sometimes have limited success in eliminating S. uberis as a stand-alone therapy. To address this challenge, the study objective was to investigate the VersaTile engineered endolysin NC5 as a supplemental therapy to cloxacillin in a mouse model of bovine S. uberis mastitis. NC5 was previously selected based on its intracellular killing and biofilm eradicating activity. To deliver preclinical proof-of-concept of this supplemental strategy, lactating mice were intramammarily infected with a bovine S. uberis field isolate and subsequently treated with cloxacillin (30.0 μg) combined with either a low (23.5 μg) or high (235.0 μg) dose of NC5. An antibiotic monotherapy group, as well as placebo treatment, was included as controls. Two types of responders were identified: fast (n = 17), showing response after 4-h treatment, and slow (n = 10), exhibiting no clear response at 4 h post-treatment across all groups. The high-dose combination therapy in comparison with placebo treatment impacted the hallmarks of mastitis in the fast responders by reducing (i) the bacterial load 13,000-fold (4.11 ± 0.78 Δlog10; p < 0.001), (ii) neutrophil infiltration 5.7-fold (p > 0.05), and (iii) the key pro-inflammatory chemokine IL-8 13-fold (p < 0.01). These mastitis hallmarks typically followed a dose response dependent on the amount of endolysin added. The current in vivo study complements our in vitro data and provides preclinical proof-of-concept of NC5 as an adjunct to intramammary cloxacillin treatment. KEY POINTS: • Engineered endolysin NC5 was preclinically evaluated as add-on to cloxacillin treatment. • Two types of mice (slow and fast responding) were observed. • The add-on treatment decreased bacterial load, neutrophil influx, and pro-inflammatory mediators.

A novel chimeric endolysin Cly2v shows potential in treating streptococci-induced bovine mastitis and systemic infections

Streptococcus species are important pathogens implicated in bovine mastitis, causing considerable economic losses within the global dairy industry. With the development of multidrug-resistant bacteria, it is crucial to develop novel antibiotic alternatives. Here, we constructed a novel chimeric endolysin, Cly2v, which comprises the Ply2741 CHAP domain (1-155aa) and the PlyV12 CBD domain (146-314aa). Biochemical characterization analysis indicated that Cly2v exhibits a melting temperature of 50.7°C and retains stable bactericidal activity at pH = 3-10. In vitro experiments demonstrated that Cly2v exhibited more efficient bactericidal activity against Streptococcus compared to the parental endolysin Ply2741. Cly2v (25 μg/mL) can effectively inhibit and reduce biofilms formed by Streptococcus, resulting in a 68 and 44% reduction in OD590nm for S. agalactiae X2 and S. uberis 002-1 biofilms. Notably, in a mouse mastitis model, treatment with Cly2v (50 μg/gland) led to a reduction in bacterial load by 2.16 log10CFU/ml and decreased inflammatory cytokine levels in mammary tissue. To our knowledge, this represents the first application of a chimeric endolysin in the treatment of early-stage mouse mastitis induced by streptococci. Additionally, in a systemic infection model, treatment with Cly2v (400 μg/mouse) provided protection rates of up to 100 and 78% against S. agalactiae ATCC13813 infections when challenged for 1 h and 3 h, respectively. Furthermore, a significant reduction in bacterial loads was observed in the blood and organs compared to the PBS group. In summary, Cly2v possesses significant potential as an alternative antibiotic for the treatment of streptococci-induced bovine mastitis and systemic infections.

Agents Targeting the Bacterial Cell Wall as Tools to Combat Gram-Positive Pathogens

The cell wall is an indispensable element of bacterial cells and a long-known target of many antibiotics. Penicillin, the first discovered beta-lactam antibiotic inhibiting the synthesis of cell walls, was successfully used to cure many bacterial infections. Unfortunately, pathogens eventually developed resistance to it. This started an arms race, and while novel beta-lactams, either natural or (semi)synthetic, were discovered, soon upon their application, bacteria were developing resistance. Currently, we are facing the threat of losing the race since more and more multidrug-resistant (MDR) pathogens are emerging. Therefore, there is an urgent need for developing novel approaches to combat MDR bacteria. The cell wall is a reasonable candidate for a target as it differentiates not only bacterial and human cells but also has a specific composition unique to various groups of bacteria. This ensures the safety and specificity of novel antibacterial agents that target this structure. Due to the shortage of low-molecular-weight candidates for novel antibiotics, attention was focused on peptides and proteins that possess antibacterial activity. Here, we describe proteinaceous agents of various origins that target bacterial cell wall, including bacteriocins and phage and bacterial lysins, as alternatives to classic antibiotic candidates for antimicrobial drugs. Moreover, advancements in protein chemistry and engineering currently allow for the production of stable, specific, and effective drugs. Finally, we introduce the concept of selective targeting of dangerous pathogens, exemplified by staphylococci, by agents specifically disrupting their cell walls.

Biological characterization of the phage lysin AVPL and its efficiency against Aerococcus viridans-induced mastitis in a murine model

Aerococcus viridans (A. viridans) is an important opportunistic zoonotic pathogen that poses a potential threat to the animal husbandry industry, such as cow mastitis, due to the widespread development of multidrug-resistant strains. Phage lysins have emerged as a promising alternative antibiotic treatment strategy. However, no lysins have been reported to treat A. viridans infections. In this study, the critical active domain and key active sites of the first A. viridans phage lysin AVPL were revealed. AVPL consists of an N-terminal N-acetylmuramoyl-L-alanine amidase catalytic domain and a C-terminal binding domain comprising two conserved LysM. H40, N44, E52, W68, H147, T157, F60, F64, I77, N92, Q97, H159, V160, D161, and S42 were identified as key sites for maintaining the activity of the catalytic domain. The LysM motif plays a crucial role in binding AVPL to bacterial cell wall peptidoglycan. AVPL maintains stable activity in the temperature range of 4-45°C and pH range of 4-10, and its activity is independent of the presence of metal ions. In vitro, the bactericidal effect of AVPL showed efficient bactericidal activity in milk samples, with 2 µg/mL of AVPL reducing A. viridans by approximately 2 Log10 in 1 h. Furthermore, a single dose (25 µg) of lysin AVPL significantly reduces bacterial load (approximately 2 Log10) in the mammary gland of mice, improves mastitis pathology, and reduces the concentration of inflammatory cytokines (TNF-α, IL-1β, and IL-6) in mammary tissue. Overall, this work provides a novel alternative therapeutic drug for mastitis induced by multidrug-resistant A. viridans.

IMPORTANCE

A. viridans is a zoonotic pathogen known to cause various diseases, including mastitis in dairy cows. In recent years, there has been an increase in antibiotic-resistant or multidrug-resistant strains of this pathogen. Phage lysins are an effective approach to treating infections caused by multidrug-resistant strains. This study revealed the biological properties and key active sites of the first A. viridans phage lysin named AVPL. AVPL can effectively kill multidrug-resistant A. viridans in pasteurized whole milk. Importantly, 25 μg AVPL significantly alleviates the symptoms of mouse mastitis induced by A. viridans. Overall, our results demonstrate the potential of lysin AVPL as an antimicrobial agent for the treatment of mastitis caused by A. viridans.

Bacteriophage-derived endolysins as innovative antimicrobials against bovine mastitis-causing streptococci and staphylococci: a state-of-the-art review

Bacteriophage-encoded endolysins, peptidoglycan hydrolases breaking down the Gram-positive bacterial cell wall, represent a groundbreaking class of novel antimicrobials to revolutionize the veterinary medicine field. Wild-type endolysins exhibit a modular structure, consisting of enzymatically active and cell wall-binding domains, that enable genetic engineering strategies for the creation of chimeric fusion proteins or so-called 'engineered endolysins'. This biotechnological approach has yielded variants with modified lytic spectrums, introducing new possibilities in antimicrobial development. However, the discovery of highly similar endolysins by different groups has occasionally resulted in the assignment of different names that complicate a straightforward comparison. The aim of this review was to perform a homology-based comparison of the wild-type and engineered endolysins that have been characterized in the context of bovine mastitis-causing streptococci and staphylococci, grouping homologous endolysins with ≥ 95.0% protein sequence similarity. Literature is explored by homologous groups for the wild-type endolysins, followed by a chronological examination of engineered endolysins according to their year of publication. This review concludes that the wild-type endolysins encountered persistent challenges in raw milk and in vivo settings, causing a notable shift in the field towards the engineering of endolysins. Lead candidates that display robust lytic activity are nowadays selected from screening assays that are performed under these challenging conditions, often utilizing advanced high-throughput protein engineering methods. Overall, these recent advancements suggest that endolysins will integrate into the antibiotic arsenal over the next decade, thereby innovating antimicrobial treatment against bovine mastitis-causing streptococci and staphylococci.

Pharmacokinetics and pharmacodynamics of antibacterial peptide NZX in Staphylococcus aureus mastitis mouse model

Staphylococcus aureus is associated with dairy mastitis, which causes serious economic losses to dairy farming industry. Antibacterial peptide NZX showed good antibacterial activity against S. aureus. This study aimed to evaluate pharmacokinetics and pharmacodynamics of NZX against S. aureus-induced mouse mastitis. NZX exhibited potent in vitro antibacterial activity against the test S. aureus strains (minimal inhibitory concentration (MIC): 0.23-0.46 μM), low mutant prevention concentration (MPC: 1.18-3.68 μM), and a long post antibiotic effect (PAE: 2.20-8.84 h), which was superior to those of lincomycin and ceftiofur. Antibacterial mechanisms showed that NZX could penetrate the cell membrane, resulting in obvious cell membrane perforation and morphological changes, and bind to intracellular DNA. Furthermore, NZX had a good stability in milk environment (retention rate: 85.36%, 24 h) than that in mammary homogenate (47.90%, 24 h). In mouse mastitis model, NZX (25-400 μg/gland) could significantly reduce the bacterial load of mammary tissue in a dose-dependent manner. In addition, NZX (100 μg/gland) could relieve the inflammatory symptoms of mammary tissue, and significantly decreased its pathological scores. The concentration-time curve of NZX (100 μg/gland) in the mammary tissue was plotted and the corresponding pharmacokinetic parameters were obtained by non-compartment model calculation. Those parameters of Tmax, T1/2, Cmax and AUC were 0.5 h, 35.11 h, 32.49 μg/g and 391 μg·h/g, respectively. Therefore, these results suggest that NZX could act as a promising candidate for treating dairy mastitis disease caused by S. aureus. KEY POINTS: • NZX could kill S. aureus by dual mechanism involved in membrane and DNA disruption • NZX could relieve S. aureus-induced mouse mastitis • Pharmacokinetic parameters of NZX in mouse mammary gland were obtained.

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.

Expression and characterization of novel chimeric endolysin CHAPk-SH3bk against biofilm-forming methicillin-resistant Staphylococcus aureus

The continuous evolution of antibiotic resistance in methicillin-resistant Staphylococcus aureus (MRSA) due to the misuse of antibiotics lays out the need for the development of new antimicrobials with higher activity and lower resistance. In this study, we have expressed novel chimeric endolysin CHAPk-SH3bk derived from LysK to investigate its antibacterial activity against planktonic and biofilm-forming MRSA. The molecular docking and MD simulation results identified critical amino acids (ASP47, ASP56, ARG71, and Gly74) of CHAPk domain responsible for its catalytic activity. Chimeric endolysin CHAPk-SH3bk showed an effective binding to peptidoglycan fragment using 14 hydrogen bonds. The in-vitro antibacterial assays displayed higher activity of CHAPk against planktonic MRSA with 2-log10 reduction in 2 h. Both CHAPk and CHAPk-SH3bk displayed bactericidal activity against MRSA with ∼4log10 and ∼3.5log10 reduction in 24 h. Biofilm reduction activity displayed CHAPk-SH3bk reduced 33 % and 60 % of hospital-associated ATCC®BAA-44™ and bovine origin SA1 respectively. The CHAPk treatment reduced 47 % of the preformed biofilm formed by bovine-origin MRSA SA1. This study indicates an effective reduction of preformed MRSA biofilms of human and animal origin using novel chimeric construct CHAPk-SH3bk. Stating that the combination and shuffling of different domains of phage endolysin potentially increase its bacteriolytic effectiveness against MRSA.

Role of bacteriophages in shaping gut microbial community

Phages are the most diversified and dominant members of the gut virobiota. They play a crucial role in shaping the structure and function of the gut microbial community and consequently the health of humans and animals. Phages are found mainly in the mucus, from where they can translocate to the intestinal organs and act as a modulator of gut microbiota. Understanding the vital role of phages in regulating the composition of intestinal microbiota and influencing human and animal health is an emerging area of research. The relevance of phages in the gut ecosystem is supported by substantial evidence, but the importance of phages in shaping the gut microbiota remains unclear. Although information regarding general phage ecology and development has accumulated, detailed knowledge on phage-gut microbe and phage-human interactions is lacking, and the information on the effects of phage therapy in humans remains ambiguous. In this review, we systematically assess the existing data on the structure and ecology of phages in the human and animal gut environments, their development, possible interaction, and subsequent impact on the gut ecosystem dynamics. We discuss the potential mechanisms of prophage activation and the subsequent modulation of gut bacteria. We also review the link between phages and the immune system to collect evidence on the effect of phages on shaping the gut microbial composition. Our review will improve understanding on the influence of phages in regulating the gut microbiota and the immune system and facilitate the development of phage-based therapies for maintaining a healthy and balanced gut microbiota.

Genomic and proteomic characterization of vB_SauM-UFV_DC4, a novel Staphylococcus jumbo phage

Staphylococcus aureus is one of the most relevant mastitis pathogens in dairy cattle, and the acquisition of antimicrobial resistance genes presents a significant health issue in both veterinary and human fields. Among the different strategies to tackle S. aureus infection in livestock, bacteriophages have been thoroughly investigated in the last decades; however, few specimens of the so-called jumbo phages capable of infecting S. aureus have been described. Herein, we report the biological, genomic, and structural proteomic features of the jumbo phage vB_SauM-UFV_DC4 (DC4). DC4 exhibited a remarkable killing activity against S. aureus isolated from the veterinary environment and stability at alkaline conditions (pH 4 to 12). The complete genome of DC4 is 263,185 bp (GC content: 25%), encodes 263 predicted CDSs (80% without an assigned function), 1 tRNA (Phe-tRNA), multisubunit RNA polymerase, and an RNA-dependent DNA polymerase. Moreover, comparative analysis revealed that DC4 can be considered a new viral species belonging to a new genus DC4 and showed a similar set of lytic proteins and depolymerase activity with closely related jumbo phages. The characterization of a new S. aureus jumbo phage increases our understanding of the diversity of this group and provides insights into the biotechnological potential of these viruses. KEY POINTS: • vB_SauM-UFV_DC4 is a new viral species belonging to a new genus within the class Caudoviricetes. • vB_SauM-UFV_DC4 carries a set of RNA polymerase subunits and an RNA-directed DNA polymerase. • vB_SauM-UFV_DC4 and closely related jumbo phages showed a similar set of lytic proteins.

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.

Structural and biochemical insights into the bacteriophage PlyGRCS endolysin targeting methicillin-resistant Staphylococcus aureus (MRSA) and serendipitous discovery of its interaction with a cold shock protein C (CspC)

Methicillin-resistant Staphylococcus aureus (MRSA) causes life-threatening human infections. Bacteriophage-encoded endolysins degrade the cell walls of Gram-positive bacteria by selectively hydrolyzing the peptidoglycan layer and thus are promising candidates to combat bacterial infections. PlyGRCS, the S. aureus-specific bacteriophage endolysin, contains a catalytic CHAP domain and a cell-wall binding SH3_5 domain connected by a linker. Here, we show the crystal structure of full-length PlyGRCS refined to 2.1 Å resolution. In addition, a serendipitous finding revealed that PlyGRCS binds to cold-shock protein C (CspC) by interacting with its CHAP and SH3_5 domains. CspC is an RNA chaperone that plays regulatory roles by conferring bacterial adaptability to various stress conditions. PlyGRCS has substantial lytic activity against S. aureus and showed only minimal change in its lytic activity in the presence of CspC. Whereas the PlyGRCS-CspC complex greatly reduced CspC-nucleic acid binding, the aforesaid complex may downregulate the CspC function during bacterial infection. Overall, the crystal structure and biochemical results of PlyGRCS provide a molecular basis for the bacteriolytic activity of PlyGRCS against S. aureus.

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.

Genome editing for phage design and uses for therapeutic applications

The over usage of antibiotics leads to antibiotic abuse which in turn eventually raises resistance mechanisms among wide range of pathogens. Due to lack of experimental data of efficacy of phages as potential antimicrobial and therapeutic agent and also more specific and cumbersome isolation process against specific pathogens makes it not so feasible technology to be looked as an alternative therapy. But, recent developments in genome editing techniques enables programmed nuclease enzymes that has effectively improvised our methodology to make accurate changes in the genomes of prokaryote as well as eukaryote cells. It is already strengthening our ability to improvise genetic engineering to disease identification by facilitating the creation of more precise models to identify the root cause. The present chapter discusses on improvisation of phage therapy using recent genome editing tools and also shares data on the methods of usage of phages and their derivatives like proteins and enzymes such as lysins and depolymerases, as a potential therapeutic or prophylaxis agent. Methods involved in recombinant based techniques were also discussed in this chapter. Combination of traditional approach with modern tools has led to a potential development of phage-based therapeutics in near future.

Comprehensive Approaches for the Search and Characterization of Staphylococcins

Novel and sustainable approaches are required to curb the increasing threat of antimicrobial resistance (AMR). Within the last decades, antimicrobial peptides, especially bacteriocins, have received increased attention and are being explored as suitable alternatives to antibiotics. Bacteriocins are ribosomally synthesized antimicrobial peptides produced by bacteria as a self-preservation method against competitors. Bacteriocins produced by Staphylococcus, also referred to as staphylococcins, have steadily shown great antimicrobial potential and are currently being considered promising candidates to mitigate the AMR menace. Moreover, several bacteriocin-producing Staphylococcus isolates of different species, especially coagulase-negative staphylococci (CoNS), have been described and are being targeted as a good alternative. This revision aims to help researchers in the search and characterization of staphylococcins, so we provide an up-to-date list of bacteriocin produced by Staphylococcus. Moreover, a universal nucleotide and amino acid-based phylogeny system of the well-characterized staphylococcins is proposed that could be of interest in the classification and search for these promising antimicrobials. Finally, we discuss the state of art of the staphylococcin applications and an overview of the emerging concerns.

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.

Effective Treatment of Staphylococcus aureus Intramammary Infection in a Murine Model Using the Bacteriophage Cocktail StaphLyse™

Staphylococcus aureus causes intramammary infections (IMIs), which are refractory to antibiotic treatment and frequently result in chronic mastitis. IMIs are the leading cause of conventional antibiotic use in dairy farms. Phage therapy represents an alternative to antibiotics to help better manage mastitis in cows, reducing the global spread of resistance. A mouse mastitis model of S. aureus IMI was used to study the efficacy of a new cocktail of five lytic S. aureus-specific phages (StaphLyse™), administered either via the intramammary (IMAM) route or intravenously (IV). The StaphLyse™ phage cocktail was stable in milk for up to one day at 37 °C and up to one week at 4 °C. The phage cocktail was bactericidal in vitro against S. aureus in a dose-dependent manner. A single IMAM injection of this cocktail given 8 h after infection reduced the bacterial load in the mammary glands of lactating mice infected with S. aureus, and as expected, a two-dose regimen was more effective. Prophylactic use (4 h pre-challenge) of the phage cocktail was also effective, reducing S. aureus levels by 4 log10 CFU per gram of mammary gland. These results suggest that phage therapy may be a viable alternative to traditional antibiotics for the control of S. aureus IMIs.

Chimeric Peptidoglycan Hydrolases Kill Staphylococcal Mastitis Isolates in Raw Milk and within Bovine Mammary Gland Epithelial Cells

Staphylococcus aureus is a major causative agent of bovine mastitis, a disease considered one of the most economically devastating in the dairy sector. Considering the increasing prevalence of antibiotic-resistant strains, novel therapeutic approaches efficiently targeting extra- and intracellular bacteria and featuring high activity in the presence of raw milk components are needed. Here, we have screened a library of eighty peptidoglycan hydrolases (PGHs) for high activity against S. aureus in raw bovine milk, twelve of which were selected for further characterization and comparison in time-kill assays. The bacteriocins lysostaphin and ALE-1, and the chimeric PGH M23LST(L)_SH3b2638 reduced bacterial numbers in raw milk to the detection limit within 10 min. Three CHAP-based PGHs (CHAPGH15_SH3bAle1, CHAPK_SH3bLST_H, CHAPH5_LST_H) showed gradually improving activity with increasing dilution of the raw milk. Furthermore, we demonstrated synergistic activity of CHAPGH15_SH3bAle1 and LST when used in combination. Finally, modification of four PGHs (LST, M23LST(L)_SH3b2638, CHAPK_SH3bLST, CHAPGH15_SH3bAle1) with the cell-penetrating peptide TAT significantly enhanced the eradication of intracellular S. aureus in bovine mammary alveolar cells compared to the unmodified parentals in a concentration-dependent manner.

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.

Lysostaphin: Engineering and Potentiation toward Better Applications

Lysostaphin is a potent bacteriolytic enzyme with endopeptidase activity against the common pathogen Staphylococcus aureus. By digesting the pentaglycine crossbridge in the cell wall peptidoglycan of S. aureus including the methicillin-resistant strains, lysostaphin initiates rapid lysis of planktonic and sessile cells (biofilms) and has great potential for use in agriculture, food industries, and pharmaceutical industries. In the past few decades, there have been tremendous efforts in potentiating lysostaphin for better applications in these fields, including engineering of the enzyme for higher potency and lower immunogenicity with longer-lasting effects, formulation and immobilization of the enzyme for higher stability and better durability, and recombinant expression for low-cost industrial production and in situ biocontrol. These achievements are extensively reviewed in this article focusing on applications in disease control, food preservation, surface decontamination, and pathogen detection. In addition, some basic properties of lysostaphin that have been controversial and only elucidated recently are summarized, including the substrate-binding properties, the number of zinc-binding sites, the substrate range, and the cleavage site in the pentaglycine crossbridge. Resistance to lysostaphin is also highlighted with a focus on various mechanisms. This article is concluded with a discussion on the limitations and future perspectives for the actual applications of lysostaphin.

Lactococcus lactis secreting phage lysins as a potential antimicrobial against multi-drug resistant Staphylococcus aureus

BACKGROUND

Staphylococcus aureus is an opportunistic Gram-positive bacterium that can form biofilm and become resistant to many types of antibiotics. The treatment of multi-drug resistant Staphylococcus aureus (MDRSA) infection is difficult since it possesses multiple antibiotic-resistant mechanisms. Endolysin and virion-associated peptidoglycan hydrolases (VAPGH) enzymes from bacteriophage have been identified as potential alternative antimicrobial agents. This study aimed to assess the ability of Lactococcus lactis NZ9000 secreting endolysin and VAPGH from S. aureus bacteriophage 88 to inhibit the growth of S. aureus PS 88, a MDRSA.

METHOD

Endolysin and VAPGH genes were cloned and expressed in L. lactis NZ9000 after fusion with the SPK1 signal peptide for secretion. The recombinant proteins were expressed and purified, then analyzed for antimicrobial activity using plate assay and turbidity reduction assay. In addition, the spent media of the recombinant lactococcal culture was analyzed for its ability to inhibit the growth of the S. aureus PS 88.

RESULTS

Extracellular recombinant endolysin (Endo88) and VAPGH (VAH88) was successfully expressed and secreted from L. lactis which was able to inhibit S. aureus PS 88, as shown by halozone formation on plate assays as well as inhibition of growth in the turbidity reduction assay. Moreover, it was observed that the spent media from L. lactis NZ9000 expressing Endo88 and VAH88 reduced the viability of PS 88 by up to 3.5-log reduction with Endo88 being more efficacious than VAH88. In addition, Endo88 was able to lyse all MRSA strains tested and Staphylococcus epidermidis but not the other bacteria while VAH88 could only lyse S. aureus PS 88.

CONCLUSION

Recombinant L. lactisNZ9000 expressing phage 88 endolysin may be potentially developed into a new antimicrobial agent for the treatment of MDRSA infection.

Comparative Transcriptome Analysis Reveals Differentially Expressed Genes Related to Antimicrobial Properties of Lysostaphin in Staphylococcus aureus

Comparative transcriptome analysis and de novo short-read assembly of S. aureus Newman strains revealed significant transcriptional changes in response to the exposure to triple-acting staphylolytic peptidoglycan hydrolase (PGH) 1801. Most altered transcriptions were associated with the membrane, cell wall, and related genes, including amidase, peptidase, holin, and phospholipase D/transphosphatidylase. The differential expression of genes obtained from RNA-seq was confirmed by reverse transcription quantitative PCR. Moreover, some of these gene expression changes were consistent with the observed structural perturbations at the DNA and RNA levels. These structural changes in the genes encoding membrane/cell surface proteins and altered gene expressions are the candidates for resistance to these novel antimicrobials. The findings in this study could provide insight into the design of new antimicrobial agents.

Treating Bacterial Infections with Bacteriophage-Based Enzybiotics: In Vitro, In Vivo and Clinical Application

Over the past few decades, we have witnessed a surge around the world in the emergence of antibiotic-resistant bacteria. This global health threat arose mainly due to the overuse and misuse of antibiotics as well as a relative lack of new drug classes in development pipelines. Innovative antibacterial therapeutics and strategies are, therefore, in grave need. For the last twenty years, antimicrobial enzymes encoded by bacteriophages, viruses that can lyse and kill bacteria, have gained tremendous interest. There are two classes of these phage-derived enzymes, referred to also as enzybiotics: peptidoglycan hydrolases (lysins), which degrade the bacterial peptidoglycan layer, and polysaccharide depolymerases, which target extracellular or surface polysaccharides, i.e., bacterial capsules, slime layers, biofilm matrix, or lipopolysaccharides. Their features include distinctive modes of action, high efficiency, pathogen specificity, diversity in structure and activity, low possibility of bacterial resistance development, and no observed cross-resistance with currently used antibiotics. Additionally, and unlike antibiotics, enzybiotics can target metabolically inactive persister cells. These phage-derived enzymes have been tested in various animal models to combat both Gram-positive and Gram-negative bacteria, and in recent years peptidoglycan hydrolases have entered clinical trials. Here, we review the testing and clinical use of these enzymes.

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.

Design and Selection of Engineered Lytic Proteins With Staphylococcus aureus Decolonizing Activity

Staphylococcus aureus causes various infections in humans and animals, the skin being the principal reservoir of this pathogen. The widespread occurrence of methicillin-resistant S. aureus (MRSA) limits the elimination and treatment of this pathogen. Phage lytic proteins have been proven as efficient antimicrobials against S. aureus. Here, a set of 12 engineered proteins based on endolysins were conceptualized to select the most optimal following a stepwise funnel approach assessing parameters including turbidity reduction, minimum inhibitory concentration (MIC), time-kill curves, and antibiofilm assays, as well as testing their stability in a broad range of storage conditions (pH, temperature, and ionic strength). The engineered phage lysins LysRODIΔAmi and ClyRODI-H5 showed the highest specific lytic activity (5 to 50 times higher than the rest), exhibited a shelf-life up to 6 months and remained stable at temperatures up to 50°C and in a pH range from 3 to 9. LysRODIΔAmi showed the lower MIC values against all staphylococcal strains tested. Both proteins were able to kill 6 log units of the strain S. aureus Sa9 within 5 min and could remove preformed biofilms (76 and 65%, respectively). Moreover, LysRODIΔAmi could prevent biofilm formation at low protein concentrations (0.15–0.6 μM). Due to its enhanced antibiofilm properties, LysRODIΔAmi was selected to effectively remove S. aureus contamination in both intact and disrupted keratinocyte monolayers. Notably, this protein did not demonstrate any toxicity toward human keratinocytes, even at high concentrations (22.1 μM). Finally, a pig skin ex vivo model was used to evaluate treatment of artificially contaminated pig skin using LysRODIΔAmi (16.5 μg/cm²). Following an early reduction of S. aureus, a second dose of protein completely eradicated S. aureus. Overall, our results suggest that LysRODIΔAmi is a suitable candidate as antimicrobial agent to prevent and treat staphylococcal skin infections.

Phage and phage lysins: New era of bio-preservatives and food safety agents

There has been an increase in the search and application of new antimicrobial agents as alternatives to use of chemical preservatives and antibiotic-like compounds by the food industry. The massive use of antibiotic has created a reservoir of antibiotic-resistant bacteria that find their way from farm to humans. Thus, there exists an imperative need to explore new antibacterial options and bacteriophages perfectly fit into the class of safe and potent antimicrobials. Phage bio-control has come a long way owing to advances with use of phage cocktails, recombinant phages, and phage lysins; however, there still exists unmet challenges that restrict the number of phage-based products reaching the market. Hence, further studies are required to explore for more efficient phage-based bio-control strategies that can become an integral part of food safety protocols. This review thus aims to highlight the recent developments made in the application of phages and phage enzymes covering pre-harvest as well as post-harvest usage. It further focuses on the major issues in both phage and phage lysin research hindering their optimum use while detailing out the advances made by researchers lately in this direction for full exploitation of phages and phage lysins in the food sector.

Overview of the risks of Staphylococcus aureus infections and their control by bacteriophages and bacteriophage-encoded products

Staphylococcus aureus is the leading cause of secondary infections in hospitals and a challenging pathogen in food industries. Decades after it was first reported, β-lactam-resistant S. aureus remains a subject of intense research owing to the ever-increasing issue of drug resistance. S. aureus bacteriophages (phages) or their encoded products are considered an alternative to antibiotics as they have been shown to be effective in treating some S. aureus-associated infections. In this review, we present a concise collection of the literature on the pathogenic potential of S. aureus and examine the prospects of using S. aureus phages and their encoded products as antimicrobials.

Characteristics for phage-encoded cell wall hydrolase of LysSAP27 to reduce staphylococcal food poisoning

To reduce staphylococcal food poisoning (SFP), a phage-encoded cell wall hydrolase called endolysin has emerged as an attractive antibacterial agent. In this study, the Staphylococcus aureus infecting phage vB_SauS-SAP27 (ϕSAP27) was isolated from sewage and characterized morphologically and genetically. ϕSAP27 was identified as Siphoviridae temperate phage, with a genome of 43 kbp. A ϕSAP27 endolysin named LysSAP27 was produced recombinantly in Escherichia coli. LysSAP27 exhibited the highest activity at neutral pH and a temperature of 30 °C, and its lytic activity was upregulated by calcium ions. Following optimization of the enzymatic conditions, LysSAP27 was applied to S. aureus-contaminated milk. Treatment with 2 μM LysSAP27 led to a significant bactericidal effect, corresponding to a reduction in bacterial titer by 2.8 log CFU/mL within 1 h and 3.4 log CFU/mL within 2 h. Therefore, LysSAP27 could be used as an effective antimicrobial agent to prevent SFP in food.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10068-021-00910-2.

Staphylococcal Biofilms: Challenges and Novel Therapeutic Perspectives

Staphylococci, like Staphylococcus aureus and S. epidermidis, are common colonizers of the human microbiota. While being harmless in many cases, many virulence factors result in them being opportunistic pathogens and one of the major causes of hospital-acquired infections worldwide. One of these virulence factors is the ability to form biofilms-three-dimensional communities of microorganisms embedded in an extracellular polymeric matrix (EPS). The EPS is composed of polysaccharides, proteins and extracellular DNA, and is finely regulated in response to environmental conditions. This structured environment protects the embedded bacteria from the human immune system and decreases their susceptibility to antimicrobials, making infections caused by staphylococci particularly difficult to treat. With the rise of antibiotic-resistant staphylococci, together with difficulty in removing biofilms, there is a great need for new treatment strategies. The purpose of this review is to provide an overview of our current knowledge of the stages of biofilm development and what difficulties may arise when trying to eradicate staphylococcal biofilms. Furthermore, we look into promising targets and therapeutic methods, including bacteriocins and phage-derived antibiofilm approaches.

Phage-Encoded Endolysins

Due to the global emergence of antibiotic resistance, there has been an increase in research surrounding endolysins as an alternative therapeutic. Endolysins are phage-encoded enzymes, utilized by mature phage virions to hydrolyze the cell wall from within. There is significant evidence that proves the ability of endolysins to degrade the peptidoglycan externally without the assistance of phage. Thus, their incorporation in therapeutic strategies has opened new options for therapeutic application against bacterial infections in the human and veterinary sectors, as well as within the agricultural and biotechnology sectors. While endolysins show promising results within the laboratory, it is important to document their resistance, safety, and immunogenicity for in-vivo application. This review aims to provide new insights into the synergy between endolysins and antibiotics, as well as the formulation of endolysins. Thus, it provides crucial information for clinical trials involving endolysins.

Development of a Novel Chimeric Endolysin, Lys109 With Enhanced Lytic Activity Against Staphylococcus aureus

As the incidence of antibiotic-resistant bacteria has become increased, phage endolysins are believed as one of the promising alternatives to antibiotics. However, the discovery of potent endolysin is still challenging because it is labor intensive and difficult to obtain a soluble form with high lytic activity. In this respect, the modular structures of Gram-positive endolysins can provide an opportunity to develop novel endolysins by domain rearrangement. In this study, a random domain swapping library of four different endolysins from phages infecting Staphylococcus aureus was constructed and screened to obtain engineered endolysins. The novel chimeric endolysin, Lys109 was selected and characterized for its staphylolytic activity. Lys109 exhibited greater bacterial cell lytic activity than its parental endolysins against staphylococcal planktonic cells and biofilms, showing highly improved activity in eliminating S. aureus from milk and on the surface of stainless steel. These results demonstrate that a novel chimeric endolysin with higher activity and solubility can be developed by random domain swapping and that this chimeric endolysin has a great potential as an antimicrobial agent.

Staphylococcins: an update on antimicrobial peptides produced by staphylococci and their diverse potential applications

Staphylococcins are antimicrobial peptides or proteins produced by staphylococci. They can be separated into different classes, depending on their amino acid composition, structural complexity, and steps involved in their production. In this review, an overview of the current knowledge on staphylococcins will be presented with emphasis on the information collected in the last decade, including a brief description of new peptides. Most staphylococcins characterized to date are either lantibiotics or linear class II bacteriocins. Recently, gene clusters coding for production of circular bacteriocins, sactipeptides, and thiopeptides have been mined from the genome of staphylococcal isolates. In contrast to class II bacteriocins, lantibiotics, sactipeptides, and thiopeptides undergo post-translational modifications that can be quite extensive, depending on the peptide. Few staphylococcins inhibit only some staphylococcal species, but most of them have proven to target pathogens belonging to different genera and involved in a variety of infectious diseases of clinical or agronomic importance. Therefore, these peptides exhibit potential application as anti-infective drugs in different areas. This review will also cover this diverse and remarkable potential. To be commercialized, however, staphylococcin production should be cost-effective and result in high bacteriocin yields, which are not generally achieved from the culture supernatant of their native producers. Such low yields make their production quite costly and not suitable at large industrial scale. Efforts already made to overcome this limitation, minimizing costs and time of production of some staphylococcins and employing either chemical synthesis or in vivo biosynthesis, will be addressed in this review as well. KEY POINTS: • Staphylococci produce a variety of antimicrobial peptides known as staphylococcins. • Most staphylococcins are post-translationally modified peptides. • Staphylococcins exhibit potential biotechnological applications. Graphical abstract.

Staphylococcus aureus persistence properties associated with bovine mastitis and alternative therapeutic modalities

Staphylococcus aureus is an important agent of contagious bovine intramammary infections in dairy cattle. Its ability to persist inside the udder is based on the presence of important mechanisms such as its ability to form biofilms, polysaccharide capsules small colony variants, and their ability to invade professional and nonprofessional cells, which will protect S. aureus from the innate and adaptive immune response of the cow, and from antibiotics that are no longer considered to be sufficient against S. aureus bovine mastitis. In this review, we present the recent research outlining S. aureus persistence properties inside the mammary gland, including its regulation mechanisms, and we highlight alternative therapeutic strategies that were tested against S. aureus isolated from bovine mastitis such as the use of probiotic bacteria, bacteriocins and bacteriophages. Overall, the persistence of S. aureus inside the mammary gland remains a pressing veterinary problem. A thorough understanding of staphylococcal persistence mechanisms will elucidate novel ways that can help in the identification of novel treatments.

Bacteriophages and associated endolysins in therapy and prevention of mastitis and metritis in cows: Current knowledge

Bacteriophages and the associated endolysins have been proposed as an alternative to antibiotic treatment of mastitis and metritis in cows. Many bacteriophages have been isolated and characterized with a large amount of lytic potential against the bacteria causing mastitis and metritis in cows. Several endolysins with marked lytic activity against mastitis pathogens in vitro were also produced from staphylococcal and streptococcal bacteriophages. In the few clinical studies, however, there has been marginal efficacy of bacteriophages in the therapy of mastitis caused by Staphylococcus aureus. Similarly, lytic bacteriophages have marked antimicrobial activity in vitro against E. coli strains from the uteri of postpartum dairy cows. In clinical studies, however, neither administration of bacteriophages early postpartum nor prepartum was effective in the prevention of metritis in cows. More clinical studies on the effectiveness of bacteriophages and the associated endolysins in the prevention and therapy of mastitis and metritis in cows, therefore, are needed.

Bacteriophage-Derived Endolysins Applied as Potent Biocontrol Agents to Enhance Food Safety

Endolysins, bacteriophage-encoded enzymes, have emerged as antibacterial agents that can be actively applied in food processing systems as food preservatives to control pathogens and ultimately enhance food safety. Endolysins break down bacterial peptidoglycan structures at the terminal step of the phage reproduction cycle to enable phage progeny release. In particular, endolysin treatment is a novel strategy for controlling antibiotic-resistant bacteria, which are a severe and increasingly frequent problem in the food industry. In addition, endolysins can eliminate biofilms on the surfaces of utensils. Furthermore, the cell wall-binding domain of endolysins can be used as a tool for rapidly detecting pathogens. Research to extend the use of endolysins toward Gram-negative bacteria is now being extensively conducted. This review summarizes the trends in endolysin research to date and discusses the future applications of these enzymes as novel food preservation tools in the field of food safety.

In vitro and in vivo efficacy of combinations of colistin and different endolysins against clinical strains of multi-drug resistant pathogens

The emergence of multidrug resistant (MDR) pathogenic bacteria is jeopardizing the value of antimicrobials, which had previously changed the course of medical science. In this study, we identified endolysins ElyA1 and ElyA2 (GH108-PG3 family), present in the genome of bacteriophages Ab1051Φ and Ab1052Φ, respectively. The muralytic activity of these endolysins against MDR clinical isolates (Acinetobacter baumannii, Pseudomonas aeruginosa and Klebsiella pneumoniae) was tested using the turbidity reduction assay. Minimal inhibitory concentrations (MICs) of endolysin, colistin and a combination of endolysin and colistin were determined, and the antimicrobial activity of each treatment was confirmed by time kill curves. Endolysin ElyA1 displayed activity against all 25 strains of A. baumannii and P. aeruginosa tested and against 13 out of 17 strains of K. pneumoniae. Endolysin ElyA2 did not display any such activity. The combined antimicrobial activity of colistin and ElyA1 yielded a reduction in the colistin MIC for all strains studied, except K. pneumoniae. These results were confirmed in vivo in G. mellonella survival assays and in murine skin and lung infection models. In conclusion, combining colistin (1/4 MIC) with the new endolysin ElyA1 (350 µg) enhanced the bactericidal activity of colistin in both in vitro and in vivo studies. This will potentially enable reduction of the dose of colistin used in clinical practice.

Targeting Hidden Pathogens: Cell-Penetrating Enzybiotics Eradicate Intracellular Drug-Resistant Staphylococcus aureus

Staphylococcus aureus is a major concern in human health care, mostly due to the increasing prevalence of antibiotic resistance. Intracellular localization of S. aureus plays a key role in recurrent infections by protecting the pathogens from antibiotics and immune responses. Peptidoglycan hydrolases (PGHs) are highly specific bactericidal enzymes active against both drug-sensitive and -resistant bacteria. However, PGHs able to effectively target intracellular S. aureus are not yet available. To overcome this limitation, we first screened 322 recombineered PGHs for staphylolytic activity under conditions found inside eukaryotic intracellular compartments. The most active constructs were modified by fusion to different cell-penetrating peptides (CPPs), resulting in increased uptake and enhanced intracellular killing (reduction by up to 4.5 log units) of various S. aureus strains (including methicillin-resistant S. aureus [MRSA]) in different tissue culture infection models. The combined application of synergistic PGH-CPP constructs further enhanced their intracellular efficacy. Finally, synergistically active PGH-CPP cocktails reduced the total S. aureus by more than 2.2 log units in a murine abscess model after peripheral injection. Significantly more intracellular bacteria were killed by the PGH-CPPs than by the PGHs alone. Collectively, our findings show that CPP-fused PGHs are effective novel protein therapeutics against both intracellular and drug-resistant S. aureusIMPORTANCE The increasing prevalence of antibiotic-resistant bacteria is one of the most urgent problems of our time. Staphylococcus aureus is an important human pathogen that has acquired several mechanisms to evade antibiotic treatment. In addition, S. aureus is able to invade and persist within human cells, hiding from the immune response and antibiotic therapies. For these reasons, novel antibacterial strategies against these pathogens are needed. Here, we developed lytic enzymes which are able to effectively target drug-resistant and intracellular S. aureus Fusion of these so-called enzybiotics to cell-penetrating peptides enhanced their uptake and intracellular bactericidal activity in cell culture and in an abscess mouse model. Our results suggest that cell-penetrating enzybiotics are a promising new class of therapeutics against staphylococcal infections.

Biotherapeutic Approaches in Atopic Dermatitis

The skin microbiome plays a central role in inflammatory skin disorders such as atopic dermatitis (AD). In AD patients, an imbalance between pathogenic Staphylococcus aureus (S. aureus) and resident skin symbionts creates a state of dysbiosis which induces immune dysregulation and impairs skin barrier function. There are now exciting new prospects for microbiome-based interventions for AD prevention. In the hopes of achieving sustained control and management of disease in AD patients, current emerging biotherapeutic strategies aim to harness the skin microbiome associated with health by restoring a more diverse symbiotic skin microbiome, while selectively removing pathogenic S. aureus. Examples of such strategies are demonstrated in skin microbiome transplants, phage-derived anti-S. aureus endolysins, monoclonal antibodies, and quorum sensing (QS) inhibitors. However, further understanding of the skin microbiome and its role in AD pathogenesis is still needed to understand how these biotherapeutics alter the dynamics of the microbiome community; to optimize patient selection, drug delivery, and treatment duration; overcome rapid recolonization upon treatment cessation; and improve efficacy to allow these therapeutic options to eventually reach routine clinical practice.

Recombinant of the Staphylococcal Bacteriophage Lysin CHAPk and Its Elimination against Streptococcus agalactiae Biofilms

Bovine mastitis is the most important infectious disease, causing significant losses in the dairy industry, in which Streptococcus agalactiae is a major pathogen. In this study, lysin CHAP_k, derived from bacteriophage K, was expressed heterogeneously, and its antimicrobial and anti-biofilm effects against S. agalactiae isolated from bovine mastitis were further analyzed. CHAP_k was expressed in Escherichia coli BL21 (DE3), in which the purified yield of CHAP_k was up to 14.6 mg/L with the purity of 95%. Time-killing kinetic curves showed that CHAP_k fastly killed S. agalactiae in TSB medium and in milk within 25 min (by 3.3 log₁₀ CFU/mL and 2.4 log₁₀ CFU/mL, respectively). Observation of scanning electron microscope (SEM) showed cells wrinkled and ruptured after the treatment of CHAP_k. CHAP_k effectively inhibited early biofilms by 95% in 8 × MIC, and eradicated mature biofilms by 89.4% in 16 × MIC. Moreover, CHAP_k killed 99% bacteria in mature biofilms. Confocal laser scanning microscopy (CLSM) also demonstrated the potent antimicrobial and anti-biofilm action of CHAP_k. It was firstly demonstrated CHAP_k had the characters of inhibition/elimination of S. agalactiae biofilms and killing the bacteria in biofilms. CHAP_k has the potential to develop a new antibacterial agent for mastitis treatment of S. agalactiae infections.

Phage Lytic Protein LysRODI Prevents Staphylococcal Mastitis in Mice

Phage lytic proteins are promising antimicrobials that could complement conventional antibiotics and help to combat multi-drug resistant bacteria that cause important human and animal infections. Here, we report the characterization of endolysin LysRODI (encoded by staphylophage phiIPLA-RODI) and its application as a prophylactic mastitis treatment. The main properties of LysRODI were compared with those of endolysin LysA72 (encoded by staphylophage phiIPLA35) and the chimeric protein CHAPSH3b (derived from the virion-associated peptidoglycan hydrolase HydH5 and lysostaphin). Time-kill experiments performed with Staphylococcus aureus and Staphylococcus epidermidis demonstrated that the killing rate of LysRODI and CHAPSH3b is higher than that of LysA72 (0.1 μM protein removed 10⁷ CFU/ml of S. aureus in 30 min). Of note, all proteins failed to select resistant mutants as bacterial exposure to sub-lethal concentrations of the proteins did not alter the MIC values. Additionally, LysRODI and CHAPSH3b were non-toxic in a zebrafish embryo model at concentrations near the MIC (0.5 and 0.7 μM, respectively). Moreover, these two proteins significantly reduced mortality in a zebrafish model of systemic infection. In contrast to LysRODI, the efficacy of CHAPSH3b was dose-dependent in zebrafish, requiring higher-dose treatments to achieve the maximum survival rate. For this reason, LysRODI was selected for further analysis in mice, demonstrating great efficacy to prevent mammary infections by S. aureus and S. epidermidis. Our findings strongly support the use of phage lytic proteins as a new strategy to prevent staphylococcal mastitis.

Endolysins as emerging alternative therapeutic agents to counter drug-resistant infections

Endolysins are the lytic products of bacteriophages which 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 being considered as alternative therapeutic agents because of their exceptional ability to target bacterial cells when applied externally. Endolysins have been studied against a number of drug-resistant pathogens to assess their therapeutic ability. This review focuses on the structure of endolysins in terms of cell binding and catalytic domains, lytic ability, resistance, safety, immunogenicity and future applications. It primarily reviews recent advancements made in evaluation of the therapeutic potential of endolysins, including their origin, host range, applications, and synergy with conventional and non-conventional antimicrobial agents.

Thermophile Lytic Enzyme Fusion Proteins that Target Clostridium perfringens

Clostridium perfringens is a bacterial pathogen that causes necrotic enteritis in poultry and livestock, and is a source of food poisoning and gas gangrene in humans. As the agriculture industry eliminates the use of antibiotics in animal feed, alternatives to antibiotics will be needed. Bacteriophage endolysins are enzymes used by the virus to burst their bacterial host, releasing bacteriophage particles. This type of enzyme represents a potential replacement for antibiotics controlling C. perfringens. As animal feed is often heat-treated during production of feed pellets, thermostable enzymes would be preferred for use in feed. To create thermostable endolysins that target C. perfringens, thermophile endolysin catalytic domains were fused to cell wall binding domains from different C. perfringens prophage endolysins. Three thermostable catalytic domains were used, two from prophage endolysins from two Geobacillus strains, and a third endolysin from the deep-sea thermophilic bacteriophage Geobacillus virus E2 (GVE2). These domains harbor predicted L-alanine-amidase, glucosaminidase, and L-alanine-amidase activities, respectively and degrade the peptidoglycan of the bacterial cell wall. The cell wall binding domains were from C. perfringens prophage endolysins (Phage LYtic enzymes; Ply): PlyCP18, PlyCP10, PlyCP33, PlyCP41, and PlyCP26F. The resulting fifteen chimeric proteins were more thermostable than the native C. perfringens endolysins, and killed swine and poultry disease-associated strains of C. perfringens.

Characterization of two glycosyl hydrolases, putative prophage endolysins, that target Clostridium perfringens

Clostridium perfringens, a spore-forming anaerobic bacterium, causes food poisoning and gas gangrene in humans and is an agent of necrotizing enteritis in poultry, swine and cattle. Endolysins are peptidoglycan hydrolases from bacteriophage that degrade the bacterial host cell wall causing lysis and thus harbor antimicrobial therapy potential. The genes for the PlyCP10 and PlyCP41 endolysins were found in prophage regions of the genomes from C. perfringens strains Cp10 and Cp41, respectively. The gene for PlyCP10 encodes a protein of 351 amino acids, while the gene for PlyCP41 encodes a protein of 335 amino acids. Both proteins harbor predicted glycosyl hydrolase domains. Recombinant PlyCP10 and PlyCP41 were expressed in E. coli with C-terminal His-tags, purified by nickel chromatography and characterized in vitro. PlyCP10 activity was greatest at pH 6.0, and between 50 and 100 mM NaCl. PlyCP41 activity was greatest between pH 6.5 and 7.0, and at 50 mM NaCl, with retention of activity as high as 600 mM NaCl. PlyCP10 lost most of its activity above 42°C, whereas PlyCP41 survived at 50°C for 30 min and still retained >60% activity. Both enzymes had lytic activity against 75 C. perfringens strains (isolates from poultry, swine and cattle) suggesting therapeutic potential.