A Lysozyme Murein Hydrolase with Broad-Spectrum Antibacterial Activity from Enterobacter Phage myPSH1140

Investigating novel Streptomyces bacteriophage endolysins as potential antimicrobial agents

As antibiotic resistance has become a major global threat, the World Health Organization (WHO) has urgently called for alternative strategies for control of bacterial infections. Endolysin, a phage-encoded protein, can degrade bacterial peptidoglycan (PG) and disrupt bacterial growth. According to the WHO, there are only three endolysin products currently in clinical phase development. In this study, we explore novel endolysins from Streptomyces phages as only a few of them have been experimentally characterized. Using several bioinformatics tools, we identified nine different functional domain combinations from 250 Streptomyces phages putative endolysins. LazerLemon gp35 (CHAP; LL35lys), Nabi gp26 (amidase; Nb26lys), and Tribute gp42 (PGRP/amidase; Tb42lys) were selected for experimental studies. We hypothesized that (i) the proteins of interest will have the ability to degrade purified PG, and (ii) the proteins will have potential antimicrobial activity against bacteria from families of importance in antibiotic resistance, such as ESKAPE safe relatives (Enterococcus raffinosus, Staphylococcus epidermidis, Klebsiella aerogenes, Acinetobacter baylyi, Pseudomonas putida, and Escherichia coli). LL35lys, Nb26lys, and Tb42lys exhibit PG-degrading activity on zymography and hydrolysis assay. The enzymes (100 µg/mL) can reduce PG turbidity to 32%-40%. The killing assay suggests that Tb42lys has a broader range (E. coli, P. putida, A. baylyi and K. aerogenes). While Nb26lys better attacks Gram-negative than -positive bacteria, LL35lys can only reduce the growth of the Gram-positive ESKAPE strains but does so effectively with a low MIC90 of 2 µg/mL. A higher concentration (≥300 µg/mL) of Nb26lys is needed to inhibit P. putida and K. aerogenes. From 250 putative endolysins, bioinformatic methods were used to select three putative endolysins for cloning and study: LL35lys, Nb26lys, and Tb42lys. All have shown PG-degrading activity, a critical function of endolysin. With a low MIC, LL35lys shows activity for the Gram-positive ESKAPE strains, while Nb26lys and Tb42lys are active against the Gram negatives. Therefore, endolysins from Streptomyces phages have potential as possible antimicrobial agents against ESKAPE bacteria.

IMPORTANCE

As antibiotic resistance has become a major global threat, the World Health Organization (WHO) has urgently called for alternative strategies for control of bacterial infections. Endolysin, a phage-encoded protein, can degrade bacterial peptidoglycan in the bacterial cell wall and disrupt bacterial growth. According to the WHO, there are only three endolysin products currently in clinical phase development. In this study we explored novel endolysins from Streptomyces phages as only a few of them have been experimentally characterized. Using several bioinformatics tools, we identified nine different combinations of functional enzymatic domain types from 250 Streptomyces bacteriophages possible endolysins. From these, three potential endolysins were selected for experimental characterization. All three showed positive results in degrading cell wall material and disrupting bacterial growth, indicating their potential as possible antimicrobial agents.

Broad-Spectrum Bactericidal Multifunctional Tiny Silicon-Based Nanoparticles Modified with Tannic Acid for Healing Infected Diabetic Wounds

Infected chronic wounds, in particular, diabetic wounds, are hard to heal, posing a global health concern with high morbidity and mortality rates. Diabetic full-thickness wounds infected with E. coli belong to the most difficult to heal chronic infected wounds. Here, we introduced tannic acid-modified silicon-based nanoparticles (TA-SiNPs) with broad-spectrum bactericidal activity that bacteria develop minimal resistance to, and they can effectively treat full-thickness wounds in diabetic mice infected with E. coli. Our findings indicate that these TA-SiNPs could achieve 100% antibacterial efficiency against S. aureus and 99.83% against E. coli, underlied by a positive surface charge and tannic acid groups facilitating bacterial membrane chemical composition depletion and depolarization of the membrane. In addition, we showed that spraying TA-SiNPs onto the skin wound of diabetic mice infected with E. coli resulted in wound healing with 98% closure after 12 days, in stark contrast to 49% of the control (PBS) and 68% of the one treated with Ofloxacin. Along with infection inhibition and ROS scavenging, we identified cell proliferation stimulation, inflammatory cytokine downregulation, and healing cytokine upregulation in the lesion, favoring the healing process. This study not only demonstrates the feasibility of employing silicon-based nanoparticles in diabetic wound healing for the first time, but also reports the first broad-spectrum bactericidal silicon nanodots. Furthermore, this provides novel insights into the mechanism of tannin-based nanoparticles disrupting bacterial membranes by depleting their chemical constituents. Our results highlighted that the developed TA-SiNPs are an effective nanomaterial for treating the infected chronic wounds.

Surface immobilization and properties optimization of phage hydrolase against Gram-negative bacteria

Immobilized hydrolase not only reduces the production of antibiotic-resistant bacteria, but also effectively improves the stability of hydrolase in external use. In this study, phage hydrolase LysSSE1 against Gram-negative bacteria were surface immobilized and optimized for their bactericidal activity. Different anti-pathogen surface materials were prepared, where LysSSE1 was immobilized on the glass surface with a silica-affinity peptide and into which different peptide linkers were introduced. Immobilized enzymes inserted into the natural amino acid peptide linker exhibited higher bactericidal activity, greater stability, and more consistent bactericidal performance compared to those without the peptide linker. Among these immobilized enzymes, LysSSE1-NL-SiAP1 exhibited the strongest bactericidal activity and the best repeatable bactericidal performance, which only reduced the original performance by about 5% after three bactericidal cycles. Modeling analysis suggested that the presence of peptide linker might increase the molecular flexibility of the proximal hydrolase domain to better interact with the bacterial substrate. Our surface immobilization strategy could be extended to other lytic proteins, providing support for the development of surface sterilization methods and materials.

Exploring the potential of naturally occurring antimicrobials for managing orthopedic-device-related infections

Orthopedic-device-related infections (ODRIs) are challenging clinical complications that are often exacerbated by antibiotic resistance and biofilm formation. This review explores the efficacy of naturally occurring antimicrobials - including agents sourced from bacteria, fungi, viruses, animals, plants and minerals - against pathogens common in ODRIs. The limitations of traditional antibiotic agents are presented, and innovative naturally occurring antimicrobials, such as bacteriophage therapy and antimicrobial peptides, are evaluated with respect to their interaction with conventional antibiotics and antibiofilm efficacy. The integration of these natural agents into clinical practice could revolutionize ODRI treatment strategies, offering effective alternatives to conventional antibiotics and mitigating resistance development. However, the translation of these compounds from research into the clinic may require the substantial investment of intellectual and financial resources.

Genomic Characterization of Phage ZP3 and Its Endolysin LysZP with Antimicrobial Potential against Xanthomonas oryzae pv. oryzae

Xanthomonas oryzae pv. oryzae (Xoo) is a significant bacterial pathogen responsible for outbreaks of bacterial leaf blight in rice, posing a major threat to rice cultivation worldwide. Effective management of this pathogen is crucial for ensuring rice yield and food security. In this study, we identified and characterized a novel Xoo phage, ZP3, isolated from diseased rice leaves in Zhejiang, China, which may offer new insights into biocontrol strategies against Xoo and contribute to the development of innovative approaches to combat bacterial leaf blight. Transmission electron microscopy indicated that ZP3 had a short, non-contractile tail. Genome sequencing and bioinformatic analysis showed that ZP3 had a double-stranded DNA genome with a length of 44,713 bp, a G + C content of 52.2%, and 59 predicted genes, which was similar to other OP1-type Xoo phages belonging to the genus Xipdecavirus. ZP3's endolysin LysZP was further studied for its bacteriolytic action, and the N-terminal transmembrane domain of LysZP is suggested to be a signal-arrest-release sequence that mediates the translocation of LysZP to the periplasm. Our study contributes to the understanding of phage-Xoo interactions and suggests that phage ZP3 and its endolysin LysZP could be developed into biocontrol agents against this phytopathogen.

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.

Genomic and biological characterization of bacteriophages against Enterobacter cloacae, a high-priority pathogen

Enterobacter cloacae is a clinically significant pathogen due to its multi-resistance to antibiotics, presenting a challenge in the treatment of infections. As concerns over antibiotic resistance escalate, novel therapeutic approaches have been explored. Bacteriophages, characterized by their remarkable specificity and ability to self-replicate within target bacteria, are emerging as a promising alternative therapy. In this study, we isolated and partially characterized nine lytic bacteriophages targeting E. cloacae, with two selected for comprehensive genomic analysis based on their host range and bacteriolytic activity. All identified phages exhibited a narrow host range, demonstrated stability within a temperature range of 30-60 °C, displayed pH tolerance from 3 to 10, and showed an excellent bacteriolytic capacity for up to 18 h. Notably, the fully characterized phage genomes revealed an absence of lysogenic, virulence, or antibiotic-resistance genes, positioning them as promising candidates for therapeutic intervention against E. cloacae-related diseases. Nonetheless, translating this knowledge into practical therapeutic applications mandates a deeper understanding of bacteriophage interactions within complex biological environments.

Assessing the synergistic potential of bacteriophage endolysins and antimicrobial peptides for eradicating bacterial biofilms

Phage-encoded endolysins have emerged as a potential substitute to conventional antibiotics due to their exceptional benefits including host specificity, rapid host killing, least risk of resistance. In addition to their antibacterial potency and biofilm eradication properties, endolysins are reported to exhibit synergism with other antimicrobial agents. In this study, the synergistic potency of endolysins was dissected with antimicrobial peptides to enhance their therapeutic effectiveness. Recombinantly expressed and purified bacteriophage endolysin [T7 endolysin (T7L); and T4 endolysin (T4L)] proteins have been used to evaluate the broad-spectrum antibacterial efficacy using different bacterial strains. Antibacterial/biofilm eradication studies were performed in combination with different antimicrobial peptides (AMPs) such as colistin, nisin, and polymyxin B (PMB) to assess the endolysin's antimicrobial efficacy and their synergy with AMPs. In combination with T7L, polymyxin B and colistin effectively eradicated the biofilm of Pseudomonas aeruginosa and exhibited a synergistic effect. Further, a combination of T4L and nisin displayed a synergistic effect against Staphylococcus aureus biofilms. In summary, the obtained results endorse the theme of combinational therapy consisting of endolysins and AMPs as an effective remedy against the drug-resistant bacterial biofilms that are a serious concern in healthcare settings.

Isolation and identification of a novel phage targeting clinical multidrug-resistant Corynebacterium striatum isolates

Introduction

Over the past decade, Corynebacterium striatum (C. striatum), an emerging multidrug-resistant (MDR) pathogen, has significantly challenged healthcare settings, especially those involving individuals with weakened immune systems. The rise of these superbugs necessitates innovative solutions.

Methods

This study aimed to isolate and characterize bacteriophages targeting MDR-C. striatum. Utilizing 54 MDR-C. striatum isolates from a local hospital as target strains, samples were collected from restroom puddles for phage screening. Dot Plaque and Double-layer plate Assays were employed for screening.

Results

A novel temperate bacteriophage, named CSP1, was identified through a series of procedures, including purification, genome extraction, sequencing, and one-step growth curves. CSP1 possesses a 39,752 base pair circular double-stranded DNA genome with HK97-like structural proteins and potential for site-specific recombination. It represents a new species within the unclassified Caudoviricetes class, as supported by transmission electron microscopy, genomic evolutionary analysis, and collinearity studies. Notably, CSP1 infected and lysed 21 clinical MDR-C. striatum isolates, demonstrating a wide host range. The phage remained stable in conditions ranging from -40 to 55°C, pH 4 to 12, and in 0.9% NaCl buffer, showing no cytotoxicity.

Discussion

The identification of CSP1 as the first phage targeting clinical C. striatum strains opens new possibilities in bacteriophage therapy research, and the development of diagnostic and therapeutic tools against pathogenic bacteria.

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.

A novel phage carrying capsule depolymerase effectively relieves pneumonia caused by multidrug-resistant Klebsiella aerogenes

BACKGROUND

Klebsiella aerogenes can cause ventilator-associated pneumonia by forming biofilms, and it is frequently associated with multidrug resistance. Phages are good antibiotic alternatives with unique advantages. There has been a lack of phage therapeutic explorations, kinetic studies, and interaction mechanism research targeting K. aerogenes.

METHODS

Plaque assay, transmission electron microscopy and whole-genome sequencing were used to determine the biology, morphology, and genomic characteristics of the phage. A mouse pneumonia model was constructed by intratracheal/endobronchial delivery of K. aerogenes to assess the therapeutic effect of phage in vivo. Bioinformatics analysis and a prokaryotic protein expression system were used to predict and identify a novel capsule depolymerase. Confocal laser scanning microscopy, Galleria mellonella larvae infection models and other experiments were performed to clarify the function of the capsule depolymerase.

RESULTS

A novel lytic phage (pK4-26) was isolated from hospital sewage. It was typical of the Podoviridae family and exhibited serotype specificity, high lytic activity, and high environmental adaptability. The whole genome is 40,234 bp in length and contains 49 coding domain sequences. Genomic data show that the phage does not carry antibiotic resistance, virulence, or lysogenic genes. The phage effectively lysed K. aerogenes in vivo, reducing mortality and alleviating pneumonia without promoting obvious side effects. A novel phage-derived depolymerase was predicted and proven to be able to digest the capsule, remove biofilms, reduce bacterial virulence, and sensitize the bacteria to serum killing.

CONCLUSIONS

The phage pK4-26 is a good antibiotic alternative and can effectively relieve pneumonia caused by multidrug-resistant K. aerogenes. It carries a depolymerase that removes biofilms, reduces virulence, and improves intrinsic immune sensitivity.

Characterization of the LysP2110-HolP2110 Lysis System in Ralstonia solanacearum Phage P2110

Ralstonia solanacearum, a pathogen causing widespread bacterial wilt disease in numerous crops, currently lacks an optimal control agent. Given the limitations of traditional chemical control methods, including the risk of engendering drug-resistant strains and environmental harm, there is a dire need for sustainable alternatives. One alternative is lysin proteins that selectively lyse bacteria without contributing to resistance development. This work explored the biocontrol potential of the LysP2110-HolP2110 system of Ralstonia solanacearum phage P2110. Bioinformatics analyses pinpointed this system as the primary phage-mediated host cell lysis mechanism. Our data suggest that LysP2110, a member of the Muraidase superfamily, requires HolP2110 for efficient bacterial lysis, presumably via translocation across the bacterial membrane. LysP2110 also exhibits broad-spectrum antibacterial activity in the presence of the outer membrane permeabilizer EDTA. Additionally, we identified HolP2110 as a distinct holin structure unique to the Ralstonia phages, underscoring its crucial role in controlling bacterial lysis through its effect on bacterial ATP levels. These findings provide valuable insights into the function of the LysP2110-HolP2110 lysis system and establish LysP2110 as a promising antimicrobial agent for biocontrol applications. This study underpins the potential of these findings in developing effective and environment-friendly biocontrol strategies against bacterial wilt and other crop diseases.

Acinetobacter Baumannii Phages: Past, Present and Future

Acinetobacter baumannii (A. baumannii) is one of the most common clinical pathogens and a typical multi-drug resistant (MDR) bacterium. With the increase of drug-resistant A. baumannii infections, it is urgent to find some new treatment strategies, such as phage therapy. In this paper, we described the different drug resistances of A. baumannii and some basic properties of A. baumannii phages, analyzed the interaction between phages and their hosts, and focused on A. baumannii phage therapies. Finally, we discussed the chance and challenge of phage therapy. This paper aims to provide a more comprehensive understanding of A. baumannii phages and theoretical support for the clinical application of A. baumannii phages.

Identification of Three Campylobacter Lysins and Enhancement of Their Anti-Escherichia coli Efficacy Using Colicin-Based Translocation and Receptor-Binding Domain Fusion

The emergence of multidrug-resistant Escherichia coli, which poses a major threat to public health, has motivated the development of numerous alternative antimicrobials. Lysins are bacteriophage- and bacterium-derived peptidoglycan hydrolases that represent a new antibiotic treatment targeting bacterial cell walls. However, the bactericidal effect of native lysins on Gram-negative bacteria is restricted by the presence of an outer membrane. Here, we first evaluated the antibacterial activity of three Campylobacter-derived lysins (Clysins) against E. coli. To improve their transmembrane ability and antibacterial activities, six engineered Clysins were constructed by fusing with the translocation and receptor-binding (TRB) domains from two types of colicins (colicin A [TRBA] and colicin K [TRBK]), and their biological activities were determined. Notably, engineered lysin TRBK-Cly02 exhibited the highest bactericidal activity against the E. coli BL21 strain, with a reduction of 6.22 ± 0.34 log units of cells at a concentration of 60.1 μg/mL, and formed an observable inhibition zone even at a dose of 6.01 μg. Moreover, TRBK-Cly02 killed E. coli dose dependently and exhibited the strongest bactericidal activity at pH 6. It also exhibited potential bioactivity against multidrug-resistant E. coli clinical isolates. In summary, this study identified three lysins from Campylobacter strains against E. coli, and the enhancement of their antibacterial activities by TRB domains fusion may allow them to be developed as potential alternatives to antibiotics. IMPORTANCE Three lysins from Campylobacter, namely, Clysins, were investigated, and their antibacterial activities against E. coli were determined for the first time. To overcome the restriction of the outer membrane of Gram-negative bacteria, we combined the TRB domains of colicins with these Clysins. Moreover, we discovered that the Clysins fused with TRB domains from colicin K (TRBK) killed E. coli more effectively, and this provides a new foundation for the development of novel bioengineered lysins by employing TRBK constructs that target outer membrane receptor/transport systems. One of the designed lysins, TRBK-Cly02, exhibited potent bactericidal efficacy against E. coli strains and may be used for control of multidrug-resistant clinical isolates. The results suggest that TRBK-Cly02 can be considered a potential antibacterial agent against pathogenic E. coli.