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Zhang Y, Li R, Zou G, Guo Y, Wu R, Zhou Y, Chen H, Zhou R, Lavigne R, Bergen PJ, Li J, Li J. Discovery of Antimicrobial Lysins from the "Dark Matter" of Uncharacterized Phages Using Artificial Intelligence. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2404049. [PMID: 38899839 DOI: 10.1002/advs.202404049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 05/29/2024] [Indexed: 06/21/2024]
Abstract
The rapid rise of antibiotic resistance and slow discovery of new antibiotics have threatened global health. While novel phage lysins have emerged as potential antibacterial agents, experimental screening methods for novel lysins pose significant challenges due to the enormous workload. Here, the first unified software package, namely DeepLysin, is developed to employ artificial intelligence for mining the vast genome reservoirs ("dark matter") for novel antibacterial phage lysins. Putative lysins are computationally screened from uncharacterized Staphylococcus aureus phages and 17 novel lysins are randomly selected for experimental validation. Seven candidates exhibit excellent in vitro antibacterial activity, with LLysSA9 exceeding that of the best-in-class alternative. The efficacy of LLysSA9 is further demonstrated in mouse bloodstream and wound infection models. Therefore, this study demonstrates the potential of integrating computational and experimental approaches to expedite the discovery of new antibacterial proteins for combating increasing antimicrobial resistance.
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Affiliation(s)
- Yue Zhang
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Runze Li
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Geng Zou
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yating Guo
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Renwei Wu
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yang Zhou
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huanchun Chen
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rui Zhou
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Rob Lavigne
- Department of Biosystems, Laboratory of Gene Technology, KU Leuven, Leuven, 3001, Belgium
| | - Phillip J Bergen
- Monash Biomedicine Discovery Institute, Department of Microbiology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, 3800, Australia
| | - Jian Li
- Monash Biomedicine Discovery Institute, Department of Microbiology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, 3800, Australia
| | - Jinquan Li
- National Key Laboratory of Agricultural Microbiology, Key Laboratory of Environment Correlative Dietology, College of Biomedicine and Health, Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518000, China
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2
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Mitkowski P, Jagielska E, Sabała I. Engineering of chimeric enzymes with expanded tolerance to ionic strength. Microbiol Spectr 2024; 12:e0354623. [PMID: 38695664 DOI: 10.1128/spectrum.03546-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 03/26/2024] [Indexed: 06/06/2024] Open
Abstract
Antimicrobial resistance poses a significant global threat, reaching dangerously high levels as reported by the World Health Organization. The emergence and rapid spread of new resistance mechanisms, coupled with the absence of effective treatments in recent decades, have led to thousands of deaths annually from infections caused by drug-resistant microorganisms. Consequently, there is an urgent need for the development of new compounds capable of combating antibiotic-resistant bacteria. A promising class of molecules exhibiting potent bactericidal effects is peptidoglycan hydrolases. Previously, we cloned and characterized the biochemical properties of the M23 catalytic domain of the EnpA (EnpACD) protein from Enterococcus faecalis. Unlike other enzymes within the M23 family, EnpACD demonstrates broad specificity. However, its activity is constrained under low ionic strength conditions. In this study, we present the engineering of three chimeric enzymes comprising EnpACD fused with three distinct SH3b cell wall-binding domains. These chimeras exhibit enhanced tolerance to environmental conditions and sustained activity in bovine and human serum. Furthermore, our findings demonstrate that the addition of SH3b domains influences the activity of the chimeric enzymes, thereby expanding their potential applications in combating antimicrobial resistance.IMPORTANCEThese studies demonstrate that the addition of the SH3b-binding domain to the EnpACD results in generation of chimeras with a broader tolerance to ionic strength and pH values, enabling them to remain active over a wider range of conditions. Such approach offers a relatively straightforward method for obtaining antibacterial enzymes with tailored properties and emphasizes the potential for proteins' engineering with enhanced functionality, contributing to the ongoing efforts to address antimicrobial resistance effectively.
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Affiliation(s)
- Paweł Mitkowski
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
| | - Elżbieta Jagielska
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
| | - Izabela Sabała
- International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Mossakowski Medical Research Institute Polish Academy of Sciences, Warsaw, Poland
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3
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MacNair CR, Rutherford ST, Tan MW. Alternative therapeutic strategies to treat antibiotic-resistant pathogens. Nat Rev Microbiol 2024; 22:262-275. [PMID: 38082064 DOI: 10.1038/s41579-023-00993-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/07/2023] [Indexed: 04/19/2024]
Abstract
Resistance threatens to render antibiotics - which are essential for modern medicine - ineffective, thus posing a threat to human health. The discovery of novel classes of antibiotics able to overcome resistance has been stalled for decades, with the developmental pipeline relying almost entirely on variations of existing chemical scaffolds. Unfortunately, this approach has been unable to keep pace with resistance evolution, necessitating new therapeutic strategies. In this Review, we highlight recent efforts to discover non-traditional antimicrobials, specifically describing the advantages and limitations of antimicrobial peptides and macrocycles, antibodies, bacteriophages and antisense oligonucleotides. These approaches have the potential to stem the tide of resistance by expanding the physicochemical property space and target spectrum occupied by currently approved antibiotics.
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Affiliation(s)
- Craig R MacNair
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Steven T Rutherford
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA
| | - Man-Wah Tan
- Department of Infectious Diseases, Genentech Inc., South San Francisco, CA, USA.
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Zheng T, Zhang C. Engineering strategies and challenges of endolysin as an antibacterial agent against Gram-negative bacteria. Microb Biotechnol 2024; 17:e14465. [PMID: 38593316 PMCID: PMC11003714 DOI: 10.1111/1751-7915.14465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/09/2024] [Accepted: 03/21/2024] [Indexed: 04/11/2024] Open
Abstract
Bacteriophage endolysin is a novel antibacterial agent that has attracted much attention in the prevention and control of drug-resistant bacteria due to its unique mechanism of hydrolysing peptidoglycans. Although endolysin exhibits excellent bactericidal effects on Gram-positive bacteria, the presence of the outer membrane of Gram-negative bacteria makes it difficult to lyse them extracellularly, thus limiting their application field. To enhance the extracellular activity of endolysin and facilitate its crossing through the outer membrane of Gram-negative bacteria, researchers have adopted physical, chemical, and molecular methods. This review summarizes the characterization of endolysin targeting Gram-negative bacteria, strategies for endolysin modification, and the challenges and future of engineering endolysin against Gram-negative bacteria in clinical applications, to promote the application of endolysin in the prevention and control of Gram-negative bacteria.
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Affiliation(s)
- Tianyu Zheng
- Bathurst Future Agri‐Tech InstituteQingdao Agricultural UniversityQingdaoChina
| | - Can Zhang
- College of Veterinary MedicineQingdao Agricultural UniversityQingdaoChina
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5
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Hassannia M, Naderifar M, Salamy S, Akbarizadeh MR, Mohebi S, Moghadam MT. Engineered phage enzymes against drug-resistant pathogens: a review on advances and applications. Bioprocess Biosyst Eng 2024; 47:301-312. [PMID: 37962644 DOI: 10.1007/s00449-023-02938-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 10/16/2023] [Indexed: 11/15/2023]
Abstract
In recent decades, the expansion of multi and extensively drug-resistant (MDR and XDR) bacteria has reached an alarming rate, causing serious health concerns. Infections caused by drug-resistant bacteria have been associated with morbidity and mortality, making tackling bacterial resistance an urgent and unmet challenge that needs to be addressed properly. Endolysins are phage-encoded enzymes that can specifically degrade the bacterial cell wall and lead to bacterial death. There is remarkable evidence that corroborates the unique ability of endolysins to rapidly digest the peptidoglycan particular bonds externally without the assistance of phage. Thus, their modulation in therapeutic approaches has opened new options for therapeutic applications in the fight against bacterial infections in the human and veterinary sectors, as well as within the agricultural and biotechnology areas. The use of genetically engineered phage enzymes (EPE) promises to generate endolysin variants with unique properties for prophylactic and therapeutic applications. These approaches have gained momentum to accelerate basic as well as translational phage research and the potential development of therapeutics in the near future. This review will focus on the novel knowledge into EPE and demonstrate that EPE has far better performance than natural endolysins and phages in dealing with antibiotic-resistant infections. Therefore, it provides essential information for clinical trials involving EPE.
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Affiliation(s)
- Mohadeseh Hassannia
- Department of Genetic, Faculty of Science, Islamic Azad University, Tehran, Iran
| | - Mahin Naderifar
- School of Medicine, Zabol University of Medical Sciences, Zabol, Iran
| | - Shakiba Salamy
- Department of Microbiology, Faculty of Pharmacy, Islamic Azad University, Tehran, Iran
| | | | - Samane Mohebi
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Park JM, Kim JH, Kim G, Sim HJ, Ahn SM, Choi KS, Kwon HJ. Rapid Antibacterial Activity Assessment of Chimeric Lysins. Int J Mol Sci 2024; 25:2430. [PMID: 38397110 PMCID: PMC10888538 DOI: 10.3390/ijms25042430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/16/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024] Open
Abstract
Various chimeric lysins have been developed as efficacious antibiotics against multidrug-resistant bacteria, but direct comparisons of their antibacterial activities have been difficult due to the preparation of multiple recombinant chimeric lysins. Previously, we reported an Escherichia coli cell-free expression method to better screen chimeric lysins against Staphylococcus aureus, but we still needed to increase the amounts of expressed proteins enough to be able to detect them non-isotopically for quantity comparisons. In this study, we improved the previous cell-free expression system by adding a previously reported artificial T7 terminator and reversing the different nucleotides between the T7 promoter and start codon to those of the T7 phage. The new method increased the expressed amount of chimeric lysins enough for us to detect them using Western blotting. Therefore, the qualitative comparison of activity between different chimeric lysins has become possible via the adjustment of the number of variables between samples without protein purification. We applied this method to select more active chimeric lysins derived from our previously reported chimeric lysin (ALS2). Finally, we compared the antibacterial activities of our selected chimeric lysins with reported chimeric lysins (ClyC and ClyO) and lysostaphin and determined the rank orders of antibacterial activities on different Staphylococcus aureus strains in our experimental conditions.
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Affiliation(s)
- Jin-Mi Park
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; (J.-M.P.); (J.-H.K.); (S.-M.A.)
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- GeNiner Inc., Seoul 08826, Republic of Korea
| | - Jun-Hyun Kim
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; (J.-M.P.); (J.-H.K.); (S.-M.A.)
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- GeNiner Inc., Seoul 08826, Republic of Korea
| | - Gun Kim
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- Laboratory of Pharmacology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Hun-Ju Sim
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- Laboratory of Pharmacology, Research Institute for Veterinary Science, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Sun-Min Ahn
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; (J.-M.P.); (J.-H.K.); (S.-M.A.)
| | - Kang-Seuk Choi
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- Laboratory of Avian Diseases, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea
| | - Hyuk-Joon Kwon
- Laboratory of Poultry Medicine, College of Veterinary Medicine, Seoul National University, Seoul 08826, Republic of Korea; (J.-M.P.); (J.-H.K.); (S.-M.A.)
- College of Veterinary Medicine and BK21 for Veterinary Science, Seoul National University, Seoul 08826, Republic of Korea; (G.K.); (H.-J.S.)
- GeNiner Inc., Seoul 08826, Republic of Korea
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7
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Malekian M, Fahimi H, Niri NM, Khaleghi S. Development of Novel Chimeric Endolysin Conjugated with Chitosan-Zn-Metal-Organic Framework Nanocomposites with Antibacterial Activity. Appl Biochem Biotechnol 2024; 196:616-631. [PMID: 37166650 DOI: 10.1007/s12010-023-04514-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/12/2023]
Abstract
Bacterial diseases have been considered the most crucial issue and are threatening human health all around the world. Also, resistance to antimicrobial drugs has become a big hurdle against efficient therapy. As a result, recombinant chimeric endolysin was produced in E. coli host to use as a potential antibacterial agent against bacteria resistance and replacement to conventional antibiotics in this study. Then, chitosan (C)-coated nanoscale metal-organic frameworks (CS-NMOFs) nanocomposite was synthesized as a novel nano delivery system to further improve the antibacterial activity of endolysin. After characterization of nanocomposite with analytical devices such as FT-IR, DLS, and TEM and determining the nanometric size of samples (30 nm to 90 nm), endolysin was covalently (endolysin-CS-NMOFs (C)) and non-covalently (endolysin-CS-NMOFs (NC)) conjugated to nanocomposite. Thereafter, the lytic ability, synergistic interaction, and biofilm reduction manner of endolysin-containing CS-NMOF nanocomposites were evaluated on E. coli, S. aureus, and P. aeruginosa strains. The results depicted an excellent lytic ability of nanocomposites after 24 h and 48 h of treatment, especially endolysin-CS-NMOFs (NC) on E. coli and P. aeruginosa strains. The synergistic interaction between nanocomposite and vancomycin did not attain for P. aeruginosa strain whereas the reverse was true for E. coli and S. aureus strains at 8 ng/mL concentration. Next, nanocomposites demonstrated potential biofilm reduction activities in various strains, especially in S. aureus and P. aeruginosa. Ultimately, our outputs demonstrate an efficient performance of the synthesized nanocomposite as an appropriate substitution for conventional antibiotics against bacteria.
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Affiliation(s)
- Mahnaz Malekian
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Hossein Fahimi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Neda Mousavi Niri
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sepideh Khaleghi
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran.
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8
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Abbasi P, Fahimi H, Khaleghi S. Novel Chimeric Endolysin Conjugated Chitosan Nanocomplex as a Potential Inhibitor Against Gram-Positive and Gram-Negative Bacteria. Appl Biochem Biotechnol 2024; 196:478-490. [PMID: 37140784 DOI: 10.1007/s12010-023-04484-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/11/2023] [Indexed: 05/05/2023]
Abstract
Resistance to antimicrobial agents has created potential problems in finding efficient treatments against bacteria. Thus, using new therapeutics, such as recombinant chimeric endolysin, would be more beneficial for eliminating resistant bacteria. The treatment ability of these therapeutics can be further improved if they are used with biocompatible nanoparticles like chitosan (CS). In this work, covalently conjugated chimeric endolysin to CS nanoparticles (C) and non-covalently entrapped endolysin in CS nanoparticles (NC) were effectively developed and, consequently, qualified and quantified using analytical devices, including FT-IR, dynamic light scattering, and TEM. Eighty to 150 nm and 100 nm to 200 nm in diameter were measured for CS-endolysin (NC) and CS-endolysin (C) using a TEM, respectively. The lytic activity, synergistic interaction, and biofilm reduction potency of nano-complexes were investigated on Escherichia coli (E. coli), Staphylococcus aureus (S. aureus), and Pseudomonas aeruginosa (P. aeruginosa) strains. The outputs revealed a good lytic activity of nano-complexes after 24 h and 48 h of treatment, especially in P. aeruginosa (approximately 40% cell viability after 48 h of treatment with 8 ng/mL), and potential biofilm reduction performance was attained in E. coli strains (about 70% reduction after treatment with 8 ng/mL). The synergistic interaction between nano-complexes and vancomycin was exhibited in E. coli, P. aeruginosa, and S. aureus strains at 8 ng/mL concentrations, while the synergistic effects of pure endolysin and vancomycin were not remarkable in E. coli strains. These nano-complexes would be more beneficial in suppressing the bacteria with a high level of antibiotic resistance.
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Affiliation(s)
- Paria Abbasi
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, 1916893813, Iran
| | - Hossein Fahimi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Sepideh Khaleghi
- Department of Biotechnology, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, 1916893813, Iran.
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9
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Vander Elst N, Bert J, Favoreel H, Lavigne R, Meyer E, Briers Y. Development of engineered endolysins with in vitro intracellular activity against streptococcal bovine mastitis-causing pathogens. Microb Biotechnol 2023; 16:2367-2386. [PMID: 37853918 PMCID: PMC10686134 DOI: 10.1111/1751-7915.14339] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 08/25/2023] [Accepted: 09/08/2023] [Indexed: 10/20/2023] Open
Abstract
Bacteriophage-derived endolysins are a novel class of antimicrobials known to rapidly kill bacteria, including antibiotic-resistant strains. We here engineered endolysins against the bovine mastitis pathogens Streptococcus uberis, Streptococcus agalactiae and Streptococcus dysgalactiae, also targeting intracellular survival and biofilm formation. For this purpose, high-throughput DNA assembly was used to create a library with >80,000 theoretical endolysin variants for screening of their bacteriolytic activity against Gram-positive isolates from (sub)clinically affected cows. This lytic activity was evaluated by turbidity reduction and time-kill assays in phosphate-buffered saline and pasteurized whole cow's milk to allow a rank up of the most potent leading candidates. A top candidate was selected with a 4.0 log killing efficacy against S. uberis, also showing similar activity against S. agalactiae and S. dysgalactiae. This top candidate eradicated S. uberis biofilm and showed intracellular activity in two bovine mammary epithelial cell lines as was confirmed by confocal microscopy. A potentiating effect on cloxacillin, a beta-lactam penicillin used to intramammarily treat bovine Gram-positive mastitis, was observed for this top candidate endolysin in raw cow's milk from (sub)clinically infected udders. Our in vitro results indicate that engineered endolysins may have a future role as add-on in the treatment of bovine streptococcal mastitis.
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Affiliation(s)
- Niels Vander Elst
- Laboratory of Gene Technology, Department of Biosystems, Faculty of Bioscience EngineeringKU LeuvenHeverleeBelgium
- Laboratory of Biochemistry, Department of Veterinary and Biosciences, Faculty of Veterinary MedicineGhent UniversityMerelbekeBelgium
- Laboratory of Applied Biotechnology, Department of Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Joni Bert
- Laboratory of Biochemistry, Department of Veterinary and Biosciences, Faculty of Veterinary MedicineGhent UniversityMerelbekeBelgium
- Laboratory of Applied Biotechnology, Department of Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
| | - Herman Favoreel
- Laboratory of Immunology, Department of Translational Physiology, Infectiology and Public Health, Faculty of Veterinary MedicineGhent UniversityMerelbekeBelgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Faculty of Bioscience EngineeringKU LeuvenHeverleeBelgium
| | - Evelyne Meyer
- Laboratory of Biochemistry, Department of Veterinary and Biosciences, Faculty of Veterinary MedicineGhent UniversityMerelbekeBelgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
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Xi H, Fu Y, Chen C, Feng X, Han W, Gu J, Ji Y. Aerococcus viridans Phage Lysin AVPL Had Lytic Activity against Streptococcus suis in a Mouse Bacteremia Model. Int J Mol Sci 2023; 24:16670. [PMID: 38068990 PMCID: PMC10706753 DOI: 10.3390/ijms242316670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/19/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Streptococcus suis (S. suis) is a swine pathogen that can cause sepsis, meningitis, endocarditis, and other infectious diseases; it is also a zoonotic pathogen that has caused a global surge in fatal human infections. The widespread prevalence of multidrug-resistant S. suis strains and the decline in novel antibiotic candidates have necessitated the development of alternative antimicrobial agents. In this study, AVPL, the Aerococcus viridans (A. viridans) phage lysin, was found to exhibit efficient bactericidal activity and broad lytic activity against multiple serotypes of S. suis. A final concentration of 300 μg/mL AVPL reduced S. suis counts by 4-4.5 log10 within 1 h in vitro. Importantly, AVPL effectively inhibited 48 h S. suis biofilm formation and disrupted preformed biofilms. In a mouse model, 300 μg/mouse AVPL protected 100% of mice from infection following the administration of lethal doses of multidrug-resistant S. suis type 2 (SS2) strain SC19, reduced the bacterial load in different organs, and effectively alleviated inflammation and histopathological damage in infected mice. These data suggest that AVPL is a valuable candidate antimicrobial agent for treating S. suis infections.
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Affiliation(s)
- Hengyu Xi
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (H.X.); (Y.F.); (C.C.); (W.H.); (J.G.)
| | - Yao Fu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (H.X.); (Y.F.); (C.C.); (W.H.); (J.G.)
| | - Chong Chen
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (H.X.); (Y.F.); (C.C.); (W.H.); (J.G.)
| | - Xin Feng
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (H.X.); (Y.F.); (C.C.); (W.H.); (J.G.)
| | - Wenyu Han
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (H.X.); (Y.F.); (C.C.); (W.H.); (J.G.)
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Jingmin Gu
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (H.X.); (Y.F.); (C.C.); (W.H.); (J.G.)
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
| | - Yalu Ji
- State Key Laboratory for Diagnosis and Treatment of Severe Zoonotic Infectious Diseases, Key Laboratory for Zoonosis Research of the Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China; (H.X.); (Y.F.); (C.C.); (W.H.); (J.G.)
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Khan FM, Chen JH, Zhang R, Liu B. A comprehensive review of the applications of bacteriophage-derived endolysins for foodborne bacterial pathogens and food safety: recent advances, challenges, and future perspective. Front Microbiol 2023; 14:1259210. [PMID: 37869651 PMCID: PMC10588457 DOI: 10.3389/fmicb.2023.1259210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/20/2023] [Indexed: 10/24/2023] Open
Abstract
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.
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Affiliation(s)
- Fazal Mehmood Khan
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, China
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
| | - Jie-Hua Chen
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Bin Liu
- Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China
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12
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Nazir A, Xu X, Liu Y, Chen Y. Phage Endolysins: Advances in the World of Food Safety. Cells 2023; 12:2169. [PMID: 37681901 PMCID: PMC10486871 DOI: 10.3390/cells12172169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/19/2023] [Accepted: 08/23/2023] [Indexed: 09/09/2023] Open
Abstract
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.
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Affiliation(s)
- Amina Nazir
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (A.N.); (X.X.); (Y.L.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
| | - Xiaohui Xu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (A.N.); (X.X.); (Y.L.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
| | - Yuqing Liu
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (A.N.); (X.X.); (Y.L.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
| | - Yibao Chen
- Shandong Key Laboratory of Animal Disease Control and Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan 250100, China; (A.N.); (X.X.); (Y.L.)
- Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Jinan 250100, China
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13
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Duan XC, Li XX, Li XM, Wang S, Zhang FQ, Qian P. Exploiting Broad-Spectrum Chimeric Lysin to Cooperate with Mupirocin against Staphylococcus aureus-Induced Skin Infections and Delay the Development of Mupirocin Resistance. Microbiol Spectr 2023; 11:e0505022. [PMID: 37125939 PMCID: PMC10269905 DOI: 10.1128/spectrum.05050-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 04/10/2023] [Indexed: 05/02/2023] Open
Abstract
Staphylococcus aureus often leads to severe skin infections. However, S. aureus is facing a crisis of antibiotic resistance. The combination of phage and antibiotics is effective for drug-resistant S. aureus infections. Therefore, it is worth exploiting novel antibacterial agents to cooperate with antibiotics against S. aureus infections. Herein, a novel chimeric lysin ClyQ was constructed, which was composed of a cysteine- and histidine-dependent amidohydrolase/peptidase (CHAP) catalytic domain from S. aureus phage lysin LysGH15 and cell wall-binding domain (CBD) from Enterococcus faecalis phage lysin PlyV12. ClyQ had an exceptionally broad host range targeting streptococci, staphylococci, E. faecalis, and E. rhusiopathiae. ClyQ combined with mupirocin (2.64 log reduction) was more effective at treating S. aureus skin infections than ClyQ (0.46 log reduction) and mupirocin (2.23 log reduction) alone. Of equal importance, none of S. aureus ATCC 29213 or S3 exposed to ClyQ developed resistance, and the combination of ClyQ and mupirocin delayed the development of mupirocin resistance. Collectively, chimeric lysin ClyQ enriches the reservoirs for treating S. aureus infections. Our findings may provide a way to alleviate the current antibiotic resistance crisis. IMPORTANCE Staphylococcus aureus, as an Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species (ESKAPE) pathogen, can escape the elimination of existing antibiotics. At present, phages and phage lysins against S. aureus infections are considered alternative antibacterial agents. However, the development of broad-spectrum chimeric phage lysins to cooperate with antibiotics against S. aureus infections remains at its initial stage. In this study, we found that the broad-host-range chimeric lysin ClyQ can synergize with mupirocin to treat S. aureus skin infections. Furthermore, the development of S. aureus resistance to mupirocin is delayed by the combination of ClyQ and mupirocin in vitro. Our results bring research attention toward the development of chimeric lysin that cooperates with antibiotics to overcome bacterial infections.
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Affiliation(s)
- Xiao-chao Duan
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xin-xin Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Xiang-min Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Shuang Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Fen-qiang Zhang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
| | - Ping Qian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Preventive Veterinary Medicine in Hubei Province, The Cooperative Innovation Center for Sustainable Pig Production, Wuhan, China
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14
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Zhang H, Zhang X, Liang S, Wang J, Zhu Y, Zhang W, Liu S, Schwarz S, Xie F. Bactericidal synergism between phage endolysin Ply2660 and cathelicidin LL-37 against vancomycin-resistant Enterococcus faecalis biofilms. NPJ Biofilms Microbiomes 2023; 9:16. [PMID: 37024490 PMCID: PMC10078070 DOI: 10.1038/s41522-023-00385-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 03/23/2023] [Indexed: 04/08/2023] Open
Abstract
Antibiotic resistance and the ability to form biofilms of Enterococcus faecalis have compromised the choice of therapeutic options, which triggered the search for new therapeutic strategies, such as the use of phage endolysins and antimicrobial peptides. However, few studies have addressed the synergistic relationship between these two promising options. Here, we investigated the combination of the phage endolysin Ply2660 and the antimicrobial peptide LL-37 to target drug-resistant biofilm-producing E. faecalis. In vitro bactericidal assays were used to demonstrate the efficacy of the Ply2660-LL-37 combination against E. faecalis. Larger reductions in viable cell counts were observed when Ply2660 and LL-37 were applied together than after individual treatment with either substance. Transmission electron microscopy revealed that the Ply2660-LL-37 combination could lead to severe cell lysis of E. faecalis. The mode of action of the Ply2660-LL-37 combination against E. faecalis was that Ply2660 degrades cell wall peptidoglycan, and subsequently, LL-37 destroys the cytoplasmic membrane. Furthermore, Ply2660 and LL-37 act synergistically to inhibit the biofilm formation of E. faecalis. The Ply2660-LL-37 combination also showed a synergistic effect for the treatment of established biofilm, as biofilm killing with this combination was superior to each substance alone. In a murine peritoneal septicemia model, the Ply2660-LL-37 combination distinctly suppressed the dissemination of E. faecalis isolates and attenuated organ injury, being more effective than each treatment alone. Altogether, our findings indicate that the combination of a phage endolysin and an antimicrobial peptide may be a potential antimicrobial strategy for combating E. faecalis.
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Affiliation(s)
- Huihui Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Xinyuan Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Siyu Liang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Jing Wang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Yao Zhu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Wanjiang Zhang
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Siguo Liu
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany.
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163, Berlin, Germany.
| | - Fang Xie
- State Key Laboratory for Animal Disease Control and Prevention, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China.
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15
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Mehmood Khan F, Manohar P, Singh Gondil V, Mehra N, Kayode Oyejobi G, Odiwuor N, Ahmad T, Huang G. The applications of animal models in phage therapy: An update. Hum Vaccin Immunother 2023; 19:2175519. [PMID: 36935353 PMCID: PMC10072079 DOI: 10.1080/21645515.2023.2175519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2023] Open
Abstract
The rapid increase in antibiotic resistance presents a dire situation necessitating the need for alternative therapeutic agents. Among the current alternative therapies, phage therapy (PT) is promising. This review extensively summarizes preclinical PT approaches in various in-vivo models. PT has been evaluated in several recent clinical trials. However, there are still several unanswered concerns due to a lack of appropriate regulation and pharmacokinetic data regarding the application of phages in human therapeutic procedures. In this review, we also presented the current state of PT and considered how animal models can be used to adapt these therapies for humans. The development of realistic solutions to circumvent these constraints is critical for advancing this technology.
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Affiliation(s)
- Fazal Mehmood Khan
- College of Civil and Transportation Engineering, Shenzhen University, Shenzhen, China.,Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China.,Institute for Innovative Development of Food Industry, Shenzhen University, Shenzhen, China.,Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Prasanth Manohar
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Vijay Singh Gondil
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.,Department of Microbiology and Immunology, University of Rochester School of Medicine and Dentistry, Rochester, New York, USA
| | - Nancy Mehra
- Department of Pediatrics, Advanced Pediatrics Centre, Postgraduate Institute of Medical Education and Research, Chandigarh, India
| | - Greater Kayode Oyejobi
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.,Department of Microbiology, Osun State University, Osogbo, Nigeria.,School of Pharmaceutical Sciences, Wuhan University, Wuhan, Hubei, China
| | - Nelson Odiwuor
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei, China.,International College, University of Chinese Academy of Sciences, Beijing, China.,Microbiology, Sino-Africa Joint Research Centre, Nairobi, Kenya
| | - Tauseef Ahmad
- Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing, China
| | - Guangtao Huang
- Department of Burn and Plastic Surgery, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen, China.,Department of Burns and Plastic Surgery, Affiliated Hospital of Zunyi Medical University, Zunyi, China.,Department of Plastic and Reconstructive Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
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16
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Tyagi JL, Sharma M, Gulati K, Kairamkonda M, Kumar D, Poluri KM. Engineering of a T7 Bacteriophage Endolysin Variant with Enhanced Amidase Activity. Biochemistry 2023; 62:330-344. [PMID: 35060722 DOI: 10.1021/acs.biochem.1c00710] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The therapeutic use of bacteriophage-encoded endolysins as enzybiotics has increased significantly in recent years due to the emergence of antibiotic resistant bacteria. Phage endolysins lyse the bacteria by targeting their cell wall. Various engineering strategies are commonly used to modulate or enhance the utility of therapeutic enzymes. This study employed a structure-guided mutagenesis approach to engineer a T7 bacteriophage endolysin (T7L) with enhanced amidase activity and lysis potency via replacement of a noncatalytic gating residue (His 37). Two H37 variants (H37A and H37K) were designed and characterized comprehensively using integrated biophysical and biochemical techniques to provide mechanistic insights into their structure-stability-dynamics-activity paradigms. Among the studied proteins, cell lysis data suggested that the obtained H37A variant exhibits amidase activity (∼35%) enhanced compared to that of wild-type T7 endolysin (T7L-WT). In contrast to this, the H37K variant is highly unstable, prone to aggregation, and less active. Comparison of the structure and dynamics of the H37A variant to those of T7L-WT evidenced that the alteration at the site of H37 resulted in long-range structural perturbations, attenuated the conformational heterogeneity, and quenched the microsecond to millisecond time scale motions. Stability analysis confirmed the altered stability of H37A compared to that of its WT counterpart. All of the obtained results established that the H37A variant enhances the lysis activity by regulating the stability-activity trade-off. This study provided deeper atomic level insights into the structure-function relationships of endolysin proteins, thus aiding researchers in the rational design of engineered endolysins with enhanced therapeutic properties.
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Affiliation(s)
- Jaya Lakshmi Tyagi
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Meenakshi Sharma
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Khushboo Gulati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Manikyaprabhu Kairamkonda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
| | - Dinesh Kumar
- Centre of Biomedical Research, SGPGIMS Campus, Lucknow 226014, Uttar Pradesh, India
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India.,Centre for Nanotechnology, Indian Institute of Technology Roorkee, Roorkee 247667, Uttarakhand, India
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17
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Keller AP, Ly S, Daetwyler S, Eichenseher F, Loessner MJ, Schmelcher M. Chimeric Peptidoglycan Hydrolases Kill Staphylococcal Mastitis Isolates in Raw Milk and within Bovine Mammary Gland Epithelial Cells. Viruses 2022; 14:v14122801. [PMID: 36560804 PMCID: PMC9781970 DOI: 10.3390/v14122801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/03/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
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.
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Jaglan AB, Anand T, Verma R, Vashisth M, Virmani N, Bera BC, Vaid RK, Tripathi BN. Tracking the phage trends: A comprehensive review of applications in therapy and food production. Front Microbiol 2022; 13:993990. [PMID: 36504807 PMCID: PMC9730251 DOI: 10.3389/fmicb.2022.993990] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/05/2022] [Indexed: 11/25/2022] Open
Abstract
In the present scenario, the challenge of emerging antimicrobial resistance is affecting human health globally. The increasing incidences of multidrug-resistant infections have become harder to treat, causing high morbidity, and mortality, and are posing extensive financial loss. Limited discovery of new antibiotic molecules has further complicated the situation and has forced researchers to think and explore alternatives to antibiotics. This has led to the resurgence of the bacteriophages as an effective alternative as they have a proven history in the Eastern world where lytic bacteriophages have been used since their first implementation over a century ago. To help researchers and clinicians towards strengthening bacteriophages as a more effective, safe, and economical therapeutic alternative, the present review provides an elaborate narrative about the important aspects of bacteriophages. It abridges the prerequisite essential requirements of phage therapy, the role of phage biobank, and the details of immune responses reported while using bacteriophages in the clinical trials/compassionate grounds by examining the up-to-date case reports and their effects on the human gut microbiome. This review also discusses the potential of bacteriophages as a biocontrol agent against food-borne diseases in the food industry and aquaculture, in addition to clinical therapy. It finishes with a discussion of the major challenges, as well as phage therapy and phage-mediated biocontrols future prospects.
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Affiliation(s)
- Anu Bala Jaglan
- Department of Zoology and Aquaculture, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Taruna Anand
- ICAR – National Research Centre on Equines, Hisar, India,*Correspondence: Taruna Anand,
| | - Ravikant Verma
- Department of Zoology and Aquaculture, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Medhavi Vashisth
- Department of Molecular Biology, Biotechnology, and Bioinformatics, Chaudhary Charan Singh Haryana Agricultural University, Hisar, India
| | - Nitin Virmani
- ICAR – National Research Centre on Equines, Hisar, India
| | - B. C. Bera
- ICAR – National Research Centre on Equines, Hisar, India
| | - R. K. Vaid
- ICAR – National Research Centre on Equines, Hisar, India
| | - B. N. Tripathi
- Animal Science Division, Indian Council of Agricultural Research, Krishi Bhawan, New Delhi, India
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19
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The Mechanism of Bacterial Resistance and Potential Bacteriostatic Strategies. Antibiotics (Basel) 2022; 11:antibiotics11091215. [PMID: 36139994 PMCID: PMC9495013 DOI: 10.3390/antibiotics11091215] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 09/04/2022] [Accepted: 09/05/2022] [Indexed: 12/26/2022] Open
Abstract
Bacterial drug resistance is rapidly developing as one of the greatest threats to human health. Bacteria will adopt corresponding strategies to crack the inhibitory effect of antibiotics according to the antibacterial mechanism of antibiotics, involving the mutation of drug target, secreting hydrolase, and discharging antibiotics out of cells through an efflux pump, etc. In recent years, bacteria are found to constantly evolve new resistance mechanisms to antibiotics, including target protective protein, changes in cell morphology, and so on, endowing them with multiple defense systems against antibiotics, leading to the emergence of multi-drug resistant (MDR) bacteria and the unavailability of drugs in clinics. Correspondingly, researchers attempt to uncover the mystery of bacterial resistance to develop more convenient and effective antibacterial strategies. Although traditional antibiotics still play a significant role in the treatment of diseases caused by sensitive pathogenic bacteria, they gradually lose efficacy in the MDR bacteria. Therefore, highly effective antibacterial compounds, such as phage therapy and CRISPER-Cas precision therapy, are gaining an increasing amount of attention, and are considered to be the treatments with the moist potential with regard to resistance against MDR in the future. In this review, nine identified drug resistance mechanisms are summarized, which enhance the retention rate of bacteria under the action of antibiotics and promote the distribution of drug-resistant bacteria (DRB) in the population. Afterwards, three kinds of potential antibacterial methods are introduced, in which new antibacterial compounds exhibit broad application prospects with different action mechanisms, the phage therapy has been successfully applied to infectious diseases caused by super bacteria, and the CRISPER-Cas precision therapy as a new technology can edit drug-resistant genes in pathogenic bacteria at the gene level, with high accuracy and flexibility. These antibacterial methods will provide more options for clinical treatment, and will greatly alleviate the current drug-resistant crisis.
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20
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Wong KY, Megat Mazhar Khair MH, Song AAL, Masarudin MJ, Chong CM, In LLA, Teo MYM. Endolysins against Streptococci as an antibiotic alternative. Front Microbiol 2022; 13:935145. [PMID: 35983327 PMCID: PMC9378833 DOI: 10.3389/fmicb.2022.935145] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/07/2022] [Indexed: 11/21/2022] Open
Abstract
Multi-drug resistance has called for a race to uncover alternatives to existing antibiotics. Phage therapy is one of the explored alternatives, including the use of endolysins, which are phage-encoded peptidoglycan hydrolases responsible for bacterial lysis. Endolysins have been extensively researched in different fields, including medicine, food, and agricultural applications. While the target specificity of various endolysins varies greatly between species, this current review focuses specifically on streptococcal endolysins. Streptococcus spp. causes numerous infections, from the common strep throat to much more serious life-threatening infections such as pneumonia and meningitis. It is reported as a major crisis in various industries, causing systemic infections associated with high mortality and morbidity, as well as economic losses, especially in the agricultural industry. This review highlights the types of catalytic and cell wall-binding domains found in streptococcal endolysins and gives a comprehensive account of the lytic ability of both native and engineered streptococcal endolysins studied thus far, as well as its potential application across different industries. Finally, it gives an overview of the advantages and limitations of these enzyme-based antibiotics, which has caused the term enzybiotics to be conferred to it.
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Affiliation(s)
- Kuan Yee Wong
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
| | - Megat Hamzah Megat Mazhar Khair
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Adelene Ai-Lian Song
- Department of Microbiology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Mas Jaffri Masarudin
- Department of Cell and Molecular Biology, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Selangor, Malaysia
| | - Chou Min Chong
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Selangor, Malaysia
| | - Lionel Lian Aun In
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
- Lionel Lian Aun In,
| | - Michelle Yee Mun Teo
- Department of Biotechnology, Faculty of Applied Sciences, UCSI University, Kuala Lumpur, Malaysia
- *Correspondence: Michelle Yee Mun Teo,
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21
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Lee C, Kim H, Ryu S. Bacteriophage and endolysin engineering for biocontrol of food pathogens/pathogens in the food: recent advances and future trends. Crit Rev Food Sci Nutr 2022; 63:8919-8938. [PMID: 35400249 DOI: 10.1080/10408398.2022.2059442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Despite advances in modern technologies, various foodborne outbreaks have continuously threatened the food safety. The overuse of and abuse/misuse of antibiotics have escalated this threat due to the prevalence of multidrug-resistant (MDR) pathogens. Therefore, the development of new methodologies for controlling microbial contamination is extremely important to ensure the food safety. As an alternative to antibiotics, bacteriophages(phages) and derived endolysins have been proposed as novel, effective, and safe antimicrobial agents and applied for the prevention and/or eradication of bacterial contaminants even in foods and food processing facilities. In this review, we describe recent genetic and protein engineering tools for phages and endolysins. The major aim of engineering is to overcome limitations such as a narrow host range, low antimicrobial activity, and low stability of phages and endolysins. Phage engineering also aims to deter the emergence of phage resistance. In the case of endolysin engineering, enhanced antibacterial ability against Gram-negative and Gram-positive bacteria is another important goal. Here, we summarize the successful studies of phages and endolysins treatment in different types of food. Moreover, this review highlights the recent advances in engineering techniques for phages and endolysins, discusses existing challenges, and suggests technical opportunities for further development, especially in terms of antimicrobial agents in the food industry.
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Affiliation(s)
- Chanyoung Lee
- Department of Food and Animal Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Hyeongsoon Kim
- Department of Food and Animal Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
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22
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Özal D, Arndt A, Thomé M. Bacteriophages and related endolysins for reduction of microorganisms in the human body - a systematic review. GMS HYGIENE AND INFECTION CONTROL 2022; 17:Doc01. [PMID: 35111563 PMCID: PMC8780682 DOI: 10.3205/dgkh000404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Background: In recent years, resistance to antibiotics has become a global threat, and alternatives to antibiotics have become an area of research. The main alternative methods are briefly described in this review. However, the main focus is bacteriophage-related therapy. Bacteriophages are viruses which, due to the production of the enzyme endolysin, are able to kill bacterial host cells. Bacteriophage therapies have a long tradition. Their potential to function as antibiotics lies in their bactericidal activity and specificity in killing bacteria without infecting or affecting eukaryotic cells. Objective: To systematically review the outcomes of bacteriophage therapy in patients with bacterial infections. Methods: The MEDLINE, EMBASE, Web of Science and CENTRAL databases were searched electronically using search terms referring to bacteriophages, endolysins and antimicrobial resistance. After the literature was screened for their titles and abstracts, full-text reviews considering inclusion/exclusion criteria were performed. Data concerning patients with bacterial infections, treatment with either bacteriophages or its enzyme endolysin and their outcomes were extracted and analysed. Results: Thirteen publications were identified that met all inclusion criteria. Data extraction shows that bacteriophages or endolysins have the potential to combat bacterial infections and significantly reduce inflammatory mediators. However, 3 out of 4 randomized controlled trials revealed that there was no significant difference between phage/endolysin treated patients and control group. Significant clinical improvements were seen in cohort and case studies. A few minor side effects were reported. Conclusions: Although there are countries in which bacteriophages are prescribed as an alternative to established antibiotics, this valuable experience has yet to be examined sufficiently in clinical trials conducted to modern standards. Despite improvements in symptoms shown in the reviewed clinical trials, the infection and the bacteria themselves were rarely completely eradicated. Therefore, no definite answer can be given as to effectiveness, and further clinical trials are necessary.
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Affiliation(s)
- Dilara Özal
- Kassel School of Medicine, University of Southampton, Southampton, UK,*To whom correspondence should be addressed: Dilara Özal, Kassel School of Medicine, University of Southampton, Southampton, UK, E-mail:
| | | | - Marcus Thomé
- Kassel School of Medicine, University of Southampton, Southampton, UK,Department of Microbiology, Klinikum Kassel, Kassel, Germany
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23
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Microbial cell surface engineering for high-level synthesis of bio-products. Biotechnol Adv 2022; 55:107912. [PMID: 35041862 DOI: 10.1016/j.biotechadv.2022.107912] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/28/2021] [Accepted: 01/09/2022] [Indexed: 02/08/2023]
Abstract
Microbial cell surface layers, which mainly include the cell membrane, cell wall, periplasmic space, outer membrane, capsules, S-layers, pili, and flagella, control material exchange between the cell and the extracellular environment, and have great impact on production titers and yields of various bio-products synthesized by microbes. Recent research work has made exciting achievements in metabolic engineering using microbial cell surface components as novel regulation targets without direct modifications of the metabolic pathways of the desired products. This review article will summarize the accomplishments obtained in this emerging field, and will describe various engineering strategies that have been adopted in bacteria and yeasts for the enhancement of mass transfer across the cell surface, improvement of protein expression and folding, modulation of cell size and shape, and re-direction of cellular resources, all of which contribute to the construction of more efficient microbial cell factories toward the synthesis of a variety of bio-products. The existing problems and possible future directions will also be discussed.
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24
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Optimized Silica-Binding Peptide-Mediated Delivery of Bactericidal Lysin Efficiently Prevents Staphylococcus aureus from Adhering to Device Surfaces. Int J Mol Sci 2021; 22:ijms222212544. [PMID: 34830425 PMCID: PMC8619460 DOI: 10.3390/ijms222212544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/07/2021] [Accepted: 11/16/2021] [Indexed: 01/18/2023] Open
Abstract
Staphylococcal-associated device-related infections (DRIs) represent a significant clinical challenge causing major medical and economic sequelae. Bacterial colonization, proliferation, and biofilm formation after adherence to surfaces of the indwelling device are probably the primary cause of DRIs. To address this issue, we incorporated constructs of silica-binding peptide (SiBP) with ClyF, an anti-staphylococcal lysin, into functionalized coatings to impart bactericidal activity against planktonic and sessile Staphylococcus aureus. An optimized construct, SiBP1-ClyF, exhibited improved thermostability and staphylolytic activity compared to its parental lysin ClyF. SiBP1-ClyF-functionalized coatings were efficient in killing MRSA strain N315 (>99.999% within 1 h) and preventing the growth of static and dynamic S. aureus biofilms on various surfaces, including siliconized glass, silicone-coated latex catheter, and silicone catheter. Additionally, SiBP1-ClyF-immobilized surfaces supported normal attachment and growth of mammalian cells. Although the recycling potential and long-term stability of lysin-immobilized surfaces are still affected by the fragility of biological protein molecules, the present study provides a generic strategy for efficient delivery of bactericidal lysin to solid surfaces, which serves as a new approach to prevent the growth of antibiotic-resistant microorganisms on surfaces in hospital settings and could be adapted for other target pathogens as well.
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25
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Rahman MU, Wang W, Sun Q, Shah JA, Li C, Sun Y, Li Y, Zhang B, Chen W, Wang S. Endolysin, a Promising Solution against Antimicrobial Resistance. Antibiotics (Basel) 2021; 10:1277. [PMID: 34827215 PMCID: PMC8614784 DOI: 10.3390/antibiotics10111277] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/14/2021] [Accepted: 10/16/2021] [Indexed: 12/24/2022] Open
Abstract
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.
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Affiliation(s)
- Mujeeb ur Rahman
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Weixiao Wang
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China;
| | - Qingqing Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Junaid Ali Shah
- College of Life Sciences, Jilin University, Changchun 130012, China;
| | - Chao Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Yanmei Sun
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Yuanrui Li
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
| | - Bailing Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Nanchang University, Nanchang 330006, China;
| | - Wei Chen
- Clinical Research Center, The Second Hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing 210003, China;
| | - Shiwei Wang
- Key Laboratory of Resources Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi’an 710069, China; (M.u.R.); (Q.S.); (C.L.); (Y.S.); (Y.L.)
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26
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Nizamudeen ZA, Xerri R, Parmenter C, Suain K, Markus R, Chakrabarti L, Sottile V. Low-Power Sonication Can Alter Extracellular Vesicle Size and Properties. Cells 2021; 10:cells10092413. [PMID: 34572062 PMCID: PMC8466153 DOI: 10.3390/cells10092413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 08/20/2021] [Accepted: 09/03/2021] [Indexed: 01/02/2023] Open
Abstract
Low-power sonication is widely used to disaggregate extracellular vesicles (EVs) after isolation, however, the effects of sonication on EV samples beyond dispersion are unclear. The present study analysed the characteristics of EVs collected from mesenchymal stem cells (MSCs) after sonication, using a combination of transmission electron microscopy, direct stochastic optical reconstruction microscopy, and flow cytometry techniques. Results showed that beyond the intended disaggregation effect, sonication using the lowest power setting available was enough to alter the size distribution, membrane integrity, and uptake of EVs in cultured cells. These results point to the need for a more systematic analysis of sonication procedures to improve reproducibility in EV-based cellular experiments.
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Affiliation(s)
| | - Rachael Xerri
- School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, UK; (R.X.); (C.P.); (K.S.)
| | - Christopher Parmenter
- School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, UK; (R.X.); (C.P.); (K.S.)
| | - Kiran Suain
- School of Pharmacy, The University of Nottingham, Nottingham NG7 2RD, UK; (R.X.); (C.P.); (K.S.)
| | - Robert Markus
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, UK;
| | - Lisa Chakrabarti
- School of Veterinary Medicine and Science, Sutton Bonington Campus, The University of Nottingham, Loughborough LE12 5RD, UK;
| | - Virginie Sottile
- School of Medicine, The University of Nottingham, Nottingham NG7 2RD, UK;
- Department of Molecular Medicine, The University of Pavia, 27100 Pavia, Italy
- Correspondence:
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27
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Lee C, Kim J, Son B, Ryu S. Development of Advanced Chimeric Endolysin to Control Multidrug-Resistant Staphylococcus aureus through Domain Shuffling. ACS Infect Dis 2021; 7:2081-2092. [PMID: 34047546 DOI: 10.1021/acsinfecdis.0c00812] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The increase in the prevalence of multidrug-resistant (MDR) Staphylococcus aureus with strong biofilm-forming capacity poses a serious public health concern. Endolysins derived from bacteriophages are a promising solution for antibiotic resistance problems. However, some natural staphylococcal endolysins have several shortcomings, such as low solubility and high sequence homology among domains. To overcome these limitations, we constructed a hybrid endolysin library by swapping an enzymatically active domain (EAD) and a cell wall binding domain (CBD) of 12 natural staphylococcal endolysins. We found a novel chimeric endolysin, ClyC, which showed enhanced lytic activity against S. aureus compared to its parental endolysin forms. ClyC also exhibited strong antibacterial activity against S. aureus in various biomatrices, such as milk and blood. Moreover, the treatment of chimeric endolysin effectively eradicated biofilms of multidrug-resistant bacteria, including methicillin-resistant S. aureus (MRSA), S. epidermidis (MRSE), and S. aureus clinical isolates. In an in vivo mouse infection model, ClyC showed effective protection capability against methicillin-resistant Staphylococcus aureus (MRSA) without any toxic effects. Taken together, our data suggest that the chimeric endolysin ClyC can be considered a potential antibacterial agent against multidrug-resistant S. aureus and may have clinical relevance.
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Affiliation(s)
- Chanyoung Lee
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Jinwoo Kim
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Bokyung Son
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Republic of Korea
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28
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Ning H, Lin H, Wang J, He X, Lv X, Ju L. Characterizations of the endolysin Lys84 and its domains from phage qdsa002 with high activities against Staphylococcus aureus and its biofilms. Enzyme Microb Technol 2021; 148:109809. [PMID: 34116743 DOI: 10.1016/j.enzmictec.2021.109809] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 04/08/2021] [Accepted: 04/20/2021] [Indexed: 01/17/2023]
Abstract
Staphylococcus aureus (S. aureus), particularly methicillin-resistant S. aureus (MRSA), and its biofilms are great threats in the food industry. Bacteriophage-encoded endolysins are promising tools to inhibit pathogens and to eliminate their biofilms. In this work, a virulent phage qdsa002 against S. aureus ATCC43300 (MRSA) was isolated, and the phage's endolysin (Lys84) and its domains were expressed and purified. Morphological and genome analyses demonstrated that qdsa002 is a Twort-like phage from Myoviridae. Lys84 contains two catalytic domains (CHAP and Amidase_2) and one cell binding domain (SH3b). This endolysin exhibits a strong lytic activity against S. aureus and has a wider bactericidal spectrum than qdsa002. Moreover, Lys84 exceed 10 μM effectively removed around 90 % of the biofilms of S. aureus. Besides, CHAP and Amidase_2 domains remained 61.20 % and 59.46 % of lytic activity as well as 84.31 % and 70.11 % of anti-biofilm activity of Lys84, respectively. The lytic and anti-biofilm activities of the combination of CHAP and Amidase_2 were close to 90 % of those of Lys84. These results indicated that Lys84 and its domains might be alternative antimicrobials for controlling S. aureus and its biofilms.
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Affiliation(s)
- Houqi Ning
- College of Food Science and Engineering, Ocean University of China, No. 5, Yushan Road, Qingdao, Shandong Province, 266003, PR China
| | - Hong Lin
- College of Food Science and Engineering, Ocean University of China, No. 5, Yushan Road, Qingdao, Shandong Province, 266003, PR China
| | - Jingxue Wang
- College of Food Science and Engineering, Ocean University of China, No. 5, Yushan Road, Qingdao, Shandong Province, 266003, PR China.
| | - Xuebing He
- College of Food Science and Engineering, Ocean University of China, No. 5, Yushan Road, Qingdao, Shandong Province, 266003, PR China
| | - Xiaoqian Lv
- College of Food Science and Engineering, Ocean University of China, No. 5, Yushan Road, Qingdao, Shandong Province, 266003, PR China
| | - Lei Ju
- College of Food Science and Engineering, Ocean University of China, No. 5, Yushan Road, Qingdao, Shandong Province, 266003, PR China
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29
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Li X, Wang S, Nyaruaba R, Liu H, Yang H, Wei H. A Highly Active Chimeric Lysin with a Calcium-Enhanced Bactericidal Activity against Staphylococcus aureus In Vitro and In Vivo. Antibiotics (Basel) 2021; 10:antibiotics10040461. [PMID: 33921682 PMCID: PMC8074178 DOI: 10.3390/antibiotics10040461] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/16/2021] [Accepted: 04/17/2021] [Indexed: 01/21/2023] Open
Abstract
Lysins, including chimeric lysins, have recently been explored as novel promising alternatives to failing antibiotics in treating multi-drug resistant (MDR) pathogens, including methicillin-resistant Staphylococcus aureus (MRSA). Herein, by fusing the CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) catalytic domain from the Ply187 lysin with the non-SH3b cell-wall binding domain from the LysSA97 lysin, a new chimeric lysin ClyC was constructed with Ca2+-enhanced bactericidal activity against all S. aureus strains tested, including MRSA. Notably, treating S. aureus with 50 μg/mL of ClyC in the presence of 100 μM Ca2+ lead to a reduction of 9 Log10 (CFU/mL) in viable bacterial number, which was the first time to observe a lysin showing such a high activity. In addition, the effective concentration of ClyC could be decreased dramatically from 12 to 1 μg/mL by combination with 0.3 μg/mL of penicillin G. In a mouse model of S. aureus bacteremia, a single intraperitoneal administration of 0.1 mg/mouse of ClyC significantly improved the survival rates and reduced 2 Log10 (CFU/mL) of the bacterial burdens in the organs of the infected mice. ClyC was also found stable after lyophilization without cryoprotectants. Based on the above observations, ClyC could be a promising candidate against S. aureus infections.
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Affiliation(s)
- Xiaohong Li
- CAS Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (X.L.); (S.W.); (R.N.); (H.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shujuan Wang
- CAS Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (X.L.); (S.W.); (R.N.); (H.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Raphael Nyaruaba
- CAS Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (X.L.); (S.W.); (R.N.); (H.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan 430074, China
| | - Huan Liu
- CAS Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (X.L.); (S.W.); (R.N.); (H.L.)
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hang Yang
- CAS Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (X.L.); (S.W.); (R.N.); (H.L.)
- Correspondence: (H.Y.); (H.W.); Tel.: +86-27-51861078 (H.Y.); +86-27-51861077 (H.W.)
| | - Hongping Wei
- CAS Key Laboratory of Emerging Pathogens and Biosafety, Centre for Biosafety Mega-Sciences, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China; (X.L.); (S.W.); (R.N.); (H.L.)
- Correspondence: (H.Y.); (H.W.); Tel.: +86-27-51861078 (H.Y.); +86-27-51861077 (H.W.)
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30
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Murray E, Draper LA, Ross RP, Hill C. The Advantages and Challenges of Using Endolysins in a Clinical Setting. Viruses 2021; 13:v13040680. [PMID: 33920965 PMCID: PMC8071259 DOI: 10.3390/v13040680] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Revised: 04/09/2021] [Accepted: 04/13/2021] [Indexed: 12/15/2022] Open
Abstract
Antibiotic-resistant pathogens are increasingly more prevalent and problematic. Traditional antibiotics are no longer a viable option for dealing with these multidrug-resistant microbes and so new approaches are needed. Bacteriophage-derived proteins such as endolysins could offer one effective solution. Endolysins are bacteriophage-encoded peptidoglycan hydrolases that act to lyse bacterial cells by targeting their cell’s wall, particularly in Gram-positive bacteria due to their naturally exposed peptidoglycan layer. These lytic enzymes have received much interest from the scientific community in recent years for their specificity, mode of action, potential for engineering, and lack of resistance mechanisms. Over the past decade, a renewed interest in endolysin therapy has led to a number of successful applications. Recombinant endolysins have been shown to be effective against prominent pathogens such as MRSA, Listeria monocytogenes, Staphylococcus strains in biofilm formation, and Pseudomonas aeruginosa. Endolysins have also been studied in combination with other antimicrobials, giving a synergistic effect. Although endolysin therapy comes with some regulatory and logistical hurdles, the future looks promising, with the emergence of engineered “next-generation” lysins. This review will focus on the likelihood that endolysins will become a viable new antimicrobial therapy and the challenges that may have to be overcome along the way.
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Affiliation(s)
- Ellen Murray
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland; (E.M.); (L.A.D.); (R.P.R.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - Lorraine A. Draper
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland; (E.M.); (L.A.D.); (R.P.R.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - R. Paul Ross
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland; (E.M.); (L.A.D.); (R.P.R.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
| | - Colin Hill
- School of Microbiology, University College Cork, T12 YT20 Cork, Ireland; (E.M.); (L.A.D.); (R.P.R.)
- APC Microbiome Ireland, University College Cork, T12 YT20 Cork, Ireland
- Correspondence: ; Tel.: +353-21-4901373
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31
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Zhu Y, Yan J, Mujtaba BM, Li Y, Wei H, Huang S. The dual anti-caries effect of carboxymethyl chitosan nanogel loaded with chimeric lysin ClyR and amorphous calcium phosphate. Eur J Oral Sci 2021; 129:e12784. [PMID: 33786916 DOI: 10.1111/eos.12784] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/09/2023]
Abstract
In this study, we evaluated the anti-biofilm and anti-demineralization abilities of a novel material, CMC-ClyR-ACP nanogel, designed by loading the chimeric lysin ClyR and amorphous calcium phosphate (ACP) into a nanocarrier material carboxymethyl chitosan (CMC), in a demineralization model. Dynamic light scattering, transmission electron microscopy, and Fourier transmission infrared spectroscopy showed that CMC-ClyR-ACP nanogel was synthesized successfully. Enamel samples prepared from premolars were divided into five groups according to their treatments with: (i) double distilled water ddH2 O, (ii) CMC-ACP, (iii) CMC-ClyR-ACP, (iv) ClyR, or (v) 0.12% chlorhexidine. Streptococcus mutans was allowed to form biofilms on the teeth for two days before treatment procedures were carried out from day 3 to day 6. The relative biofilm viability analyzed by Cell Counting Kit-8 showed that it was significantly lower (at 55.7%) for CMC-ClyR-ACP than seen for ddH2 O (89.9%), which was consistent with result of confocal laser scanning microscopy. The percentage surface hardness loss of CMC-ClyR-ACP (29.2%) was significantly lower than that of CMC-ACP (51.0%) and ClyR (58.7%) alone, and there was no significant difference between CMC-ClyR-ACP and chlorhexidine (26.9%), which was confirmed by scanning electron microscopy. Therefore, CMC-ClyR-ACP nanogel may be an effective strategy for the control of enamel demineralization.
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Affiliation(s)
- Yun Zhu
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Orthodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Jiarong Yan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Orthodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Babar Muhammad Mujtaba
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Yuhong Li
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Endodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China
| | - Hongping Wei
- Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Shengfu Huang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China.,Department of Orthodontics, School & Hospital of Stomatology, Wuhan University, Wuhan, China
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32
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Zha J, Liu Z, Sun R, Gong G, Dordick JS, Wu X. Endolysin-Based Autolytic E. coli System for Facile Recovery of Recombinant Proteins. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:3134-3143. [PMID: 33656890 DOI: 10.1021/acs.jafc.1c00059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Recovery of recombinant proteins from the Escherichia coli cytoplasm depends on cell disruption by mechanical, chemical, and/or enzymatic methods, which usually cause incomplete cell breakage or protein denaturation. Controllable autolytic E. coli strains have been designed to facilitate the purification of recombinant proteins; however, these strains suffer from low recovery yield, slow cell lysis, or extensive strain engineering. Herein, we report an improved, highly efficient programmable autolytic E. coli platform, in which cell lysis is initiated upon the induced expression of T4 lysozyme with N-terminal fusion of a cell-penetrating peptide. Through the engineering of the peptide sequence and copy number, and by incorporating the fusion lytic gene into the E. coli genome, more than 99.97% of cells could be lysed within 30 min of induction regardless of cell age. We further tested the expression and release of a recombinant enzyme lysostaphin (Lst) and demonstrated that 4 h induction of the lytic gene after 3 h of Lst expression resulted in 98.97% cell lysis. Lst obtained from this system had the same yield, yet 1.63-fold higher activity, compared with that obtained from cells lysed by freeze-thawing and sonication. This autolytic platform shows potential for use in large-scale microbial production of proteins and other biopolymers.
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Affiliation(s)
- Jian Zha
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Zhiqiang Liu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Runcong Sun
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Guoli Gong
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
| | - Jonathan S Dordick
- Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, United States
| | - Xia Wu
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi'an, Shaanxi 710021, China
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Internal cell-penetrating peptide-mediated internalization enables a chimeric lysin to target intracellular pathogens. Int J Pharm 2021; 599:120449. [PMID: 33711472 DOI: 10.1016/j.ijpharm.2021.120449] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 02/11/2021] [Accepted: 02/26/2021] [Indexed: 11/21/2022]
Abstract
Intracellular pathogens pose serious challenges to the public health worldwide. Lysin, peptidoglycan hydrolase from phage, is promising alternative to conventional antibiotics because of its high bactericidal activity and low risk of resistance. However, most proteinaceous lysins cannot penetrate the mammalian cell membrane because of size exclusion. Previously, we reported a broad-spectrum chimeric lysin, ClyR, with a cysteine, histidine-dependent amidohydrolase/peptidase catalytic domain from PlyC lysin and an SH-3b cell-wall binding domain from PlySs2 lysin. Herein, we further report that a novel internal cell-penetrating peptide (CPP) is predicted in the junction region of the two constitutive domains of ClyR, mediated by which ClyR can be internalized by epithelial cells through caveolin-dependent endocytosis to target intracellular pathogens. Residues K153, P154, R169, and R188 of the internal CPP were found to be essential for ClyR-mediated internalization and intracellular killing. RNA-seq analysis further showed that there are minor differences in transcript and metabolic profiles from epithelial cells exposed to 100 μg/ml ClyR for 24 h. Taken together, our findings demonstrate a novel mechanism of internalization by ClyR, providing new insights into the rational designing of the next-generation lysins to target both extracellular and intracellular pathogens.
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34
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Khan FM, Gondil VS, Li C, Jiang M, Li J, Yu J, Wei H, Yang H. A Novel Acinetobacter baumannii Bacteriophage Endolysin LysAB54 With High Antibacterial Activity Against Multiple Gram-Negative Microbes. Front Cell Infect Microbiol 2021; 11:637313. [PMID: 33738267 PMCID: PMC7960757 DOI: 10.3389/fcimb.2021.637313] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/21/2021] [Indexed: 12/14/2022] Open
Abstract
The rapid spread and emergence of multidrug-resistant Acinetobacter baumannii and other pathogenic Gram-negative bacteria spurred scientists and clinicians to look for alternative therapeutic agents to conventional antibiotics. In the present study, an A. baumannii bacteriophage p54 was isolated and characterized. Morphological and genome analysis revealed that bacteriophage p54 belongs to Myoviridae family with a genome size of 165,813 bps. A novel endolysin, namely LysAB54, showing low similarity with other well-known related endolysins, was cloned, expressed, and characterized from the bacteriophage p54. LysAB54 showed significant bactericidal activity against multidrug-resistant A. baumannii and other Gram-negative bacteria, including Pseudomonas aeruginosa, Klebsiella pneumoniae, and Escherichia coli, in the absence of outer membrane permeabilizers. Based on all those observations, LysAB54 could represent a potential agent for the treatment of multidrug-resistant Gram-negative superbugs.
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Affiliation(s)
- Fazal Mehmood Khan
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
| | - Vijay Singh Gondil
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Changchang Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
| | - Mengwei Jiang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Junhua Li
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Junping Yu
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
| | - Hang Yang
- CAS Key Laboratory of Special Pathogens and Biosafety, Center for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China.,International College, University of Chinese Academy of Sciences, Beijing, China
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35
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Synergistic effects of endolysin Lysqdvp001 and ε-poly-lysine in controlling Vibrio parahaemolyticus and its biofilms. Int J Food Microbiol 2021; 343:109112. [PMID: 33640572 DOI: 10.1016/j.ijfoodmicro.2021.109112] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/29/2021] [Accepted: 02/10/2021] [Indexed: 11/23/2022]
Abstract
The synergistic antibacterial effects between endolysin Lysqdvp001 and ε-poly-lysine (ε-PL) against Vibrio parahaemolyticus (V. parahaemolyticus) were investigated in this study. Lysqdvp001 combined with ε-PL exhibited a strong antibacterial synergism against V. parahaemolyticus. The combinations of Lysqdvp001 (≥60 U/mL) and ε-PL (≥0.2 mg/mL) dramatically decreased cell density of the bacterial suspensions at both 25 °C and 37 °C. Surface zeta potential increment and membrane hyperpolarization of V. parahaemolyticus were observed after treatment by ε-PL and its combination with Lysqdvp001. More β-lactamase and β-galactosidase were leaked from V. parahaemolyticus with combined treatment of Lysqdvp001 and ε-PL than from the bacteria treated with single Lysqdvp001 or ε-PL. Fluorescence and transmission electron microscope revealed that Lysqdvp001 and ε-PL synergistically induced the damage and morphological destruction of V. parahaemolyticus cells. When applying in Gadus macrocephalus, Penaeus orientalis and oyster, the two antimicrobials' cocktail allowed for 3.75, 4.16 and 2.50 log10CFU/g reductions of V. parahaemolyticus, respectively. Besides, Lysqdvp001 in combination with ε-PL removed approximately 44%-68% of V. parahaemolyticus biofilms on polystyrene, glass and stainless steel surfaces. These results demonstrated that Lysqdvp001 and ε-PL might be used together for controlling V. parahaemolyticus and the bacterial biofilms in food industry.
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36
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Xu X, Zhang D, Zhou B, Zhen X, Ouyang S. Structural and biochemical analyses of the tetrameric cell binding domain of Lys170 from enterococcal phage F170/08. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:721-729. [PMID: 33609147 DOI: 10.1007/s00249-021-01511-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/11/2021] [Accepted: 02/08/2021] [Indexed: 10/22/2022]
Abstract
Lysins are a class of hydrolytic enzymes used by bacteriophages to target and cleave the peptidoglycan of bacterial cell walls during their lytic cycle. The lysins from bacteriophages that infect Gram-positive bacteria are typically monomeric and consist of one or two catalytic domains (CD) and a cell binding domain (CBD). However, multimeric lysins encoded by a single gene have also been reported, among which Lys170 from enterococcal phage F170/08 was one of the first identified. Here, we determined the crystal structure of Lys170 CBD at 1.40 Å resolution. The structure reveals that Lys170 CBDs assemble into a tetrameric functional unit and that each monomer folds into a three-stranded β-sheet core capped on each side by an α-helix. In addition, we identified key residues of Lys170 CBD involved in host cell binding. Our work provides a basis for designing highly efficient lysins targeting Enterococcus faecalis.
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Affiliation(s)
- Xiaolong Xu
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Dandan Zhang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.,The Engineering Technology Research Center of Characteristic Medicinal Plants of Fujian, Ningde Normal University, Ningde, China
| | - Biao Zhou
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Xiangkai Zhen
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.
| | - Songying Ouyang
- The Key Laboratory of Innate Immune Biology of Fujian Province, Provincial University Key Laboratory of Cellular Stress Response and Metabolic Regulation, Biomedical Research Center of South China, Key Laboratory of OptoElectronic Science and Technology for Medicine of the Ministry of Education, College of Life Sciences, Fujian Normal University, Fuzhou, China.
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37
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Linden SB, Alreja AB, Nelson DC. Application of bacteriophage-derived endolysins to combat streptococcal disease: current state and perspectives. Curr Opin Biotechnol 2021; 68:213-220. [PMID: 33529969 DOI: 10.1016/j.copbio.2021.01.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2021] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 12/20/2022]
Abstract
The decline in new antibiotic candidates combined with an increase in antibiotic-resistance necessitates development of alternative antimicrobials. Bacteriophage-encoded endolysins (lysins) are a class of peptidoglycan hydrolases that have been proposed to fill this antimicrobial void. The past 20 years has seen a dramatic expansion of studies on endolysin discovery, structure/function, engineering, immunogenicity, toxicity/safety, and efficacy in animal models. These collective efforts have led to current human clinical trials on at least three different endolysins that are antimicrobial toward staphylococcal species. It can be anticipated that endolysins targeting streptococcal species may be next in line for translational development. Notably, streptococcal diseases largely manifest at accessible mucous membranes, which should be beneficial for protein therapeutics. Additionally, there are a number of well-identified streptococcal diseases in both humans and animals that are associated with a single species, further favoring a targeted endolysin therapeutic.
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Affiliation(s)
- Sara B Linden
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Adit B Alreja
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA
| | - Daniel C Nelson
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD 20850, USA; Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA.
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38
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Abdelrahman F, Easwaran M, Daramola OI, Ragab S, Lynch S, Oduselu TJ, Khan FM, Ayobami A, Adnan F, Torrents E, Sanmukh S, El-Shibiny A. Phage-Encoded Endolysins. Antibiotics (Basel) 2021; 10:124. [PMID: 33525684 PMCID: PMC7912344 DOI: 10.3390/antibiotics10020124] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/16/2021] [Accepted: 01/26/2021] [Indexed: 12/17/2022] Open
Abstract
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.
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Affiliation(s)
- Fatma Abdelrahman
- Center for Microbiology and Phage Therapy, Biomedical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Maheswaran Easwaran
- Department of Biomedical Engineering, Sethu Institute of Technology, Tamil Nadu 626115, India
| | - Oluwasegun I Daramola
- Department of Biomedical Laboratory Science, College of Medicine, University of Ibadan, Ibadan 200284, Nigeria
| | - Samar Ragab
- Center for Microbiology and Phage Therapy, Biomedical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
| | - Stephanie Lynch
- School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia
| | - Tolulope J Oduselu
- Department of Biomedical Laboratory Science, College of Medicine, University of Ibadan, Ibadan 200284, Nigeria
| | - Fazal Mehmood Khan
- Center for Biosafety Mega-Science, Key Laboratory of Special Pathogens and Biosafety, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan 430071, China
- International College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Akomolafe Ayobami
- Department of Biomedical Laboratory Science, College of Medicine, University of Ibadan, Ibadan 200284, Nigeria
| | - Fazal Adnan
- Atta ur Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology (NUST), Islamabad 24090, Pakistan
| | - Eduard Torrents
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
- Microbiology Section, Department of Genetics, Microbiology, and Statistics, Faculty of Biology, University of Barcelona, 08028 Barcelona, Spain
| | - Swapnil Sanmukh
- Bacterial Infections: Antimicrobial Therapies Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Biomedical Sciences, Zewail City of Science and Technology, Giza 12578, Egypt
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39
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Son B, Kong M, Lee Y, Ryu S. Development of a Novel Chimeric Endolysin, Lys109 With Enhanced Lytic Activity Against Staphylococcus aureus. Front Microbiol 2021; 11:615887. [PMID: 33519773 PMCID: PMC7843465 DOI: 10.3389/fmicb.2020.615887] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2020] [Accepted: 12/16/2020] [Indexed: 01/21/2023] Open
Abstract
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.
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Affiliation(s)
- Bokyung Son
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Minsuk Kong
- Department of Food Science and Technology, Seoul National University of Science and Technology, Seoul, South Korea
| | - Yoona Lee
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Seoul National University, Seoul, South Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
- Center for Food and Bioconvergence, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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40
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A Choline-Recognizing Monomeric Lysin, ClyJ-3m, Shows Elevated Activity against Streptococcus pneumoniae. Antimicrob Agents Chemother 2020; 64:AAC.00311-20. [PMID: 32958710 DOI: 10.1128/aac.00311-20] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 09/10/2020] [Indexed: 12/29/2022] Open
Abstract
Streptococcus pneumoniae is a leading pathogen for bacterial pneumonia, which can be treated with bacteriophage lysins harboring a conserved choline binding module (CBM). Such lysins regularly function as choline-recognizing dimers. Previously, we reported a pneumococcus-specific lysin ClyJ comprising the binding domain from the putative endolysin gp20 from the Streptococcus phage SPSL1 and the CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) catalytic domain from the PlyC lysin. A variant of ClyJ with a shortened linker, i.e., ClyJ-3, shows improved activity and reduced cytotoxicity. Resembling typical CBM-containing lysins, ClyJ-3 dimerized upon binding with choline. Herein, we further report a choline-recognizing variant of ClyJ-3, i.e., ClyJ-3m, constructed by deleting its C-terminal tail. Biochemical characterization showed that ClyJ-3m remains a monomer after it binds to choline yet exhibits improved bactericidal activity against multiple pneumococcal strains with different serotypes. In an S. pneumoniae-infected bacteremia model, a single intraperitoneal administration of 2.32 μg/mouse of ClyJ-3m showed 70% protection, while only 20% of mice survived in the group receiving an equal dose of ClyJ-3 (P < 0.05). A pharmacokinetic analysis following single intravenously doses of 0.29 and 1.16 mg/kg of ClyJ-3 or ClyJ-3m in BALB/c mice revealed that ClyJ-3m shows a similar half-life but less clearance and a greater area under curve than ClyJ-3. Taken together, the choline-recognizing monomer ClyJ-3m exhibited enhanced bactericidal activity and improved pharmacokinetic proprieties compared to those of its parental ClyJ-3 lysin. Our study also provides a new way for rational design and programmed engineering of lysins targeting S. pneumoniae.
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41
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Mondal SI, Draper LA, Ross RP, Hill C. Bacteriophage endolysins as a potential weapon to combat Clostridioides difficile infection. Gut Microbes 2020; 12:1813533. [PMID: 32985336 PMCID: PMC7524323 DOI: 10.1080/19490976.2020.1813533] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Clostridioides difficile is the leading cause of health-care-associated infection throughout the developed world and contributes significantly to patient morbidity and mortality. Typically, antibiotics are used for the primary treatment of C. difficile infections (CDIs), but they are not universally effective for all ribotypes and can result in antibiotic resistance and recurrent infection, while also disrupting the microbiota. Novel targeted therapeutics are urgently needed to combat CDI. Bacteriophage-derived endolysins are required to disrupt the bacterial cell wall of their target bacteria and are possible alternatives to antibiotics. These lytic proteins could potentially replace or augment antibiotics in CDI treatment. We discuss candidate therapeutic lysins derived from phages/prophages of C. difficile and their potential as antimicrobials against CDI. Additionally, we review the antibacterial potential of some recently identified homologues of C. difficile endolysins. Finally, the challenges of endolysins are considered with respect to the development of novel lysin-based therapies.
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Affiliation(s)
- Shakhinur Islam Mondal
- APC Microbiome Ireland, University College Cork, Cork, Ireland,Genetic Engineering and Biotechnology Department, Shahjalal University of Science and Technology, Sylhet, Bangladesh
| | - Lorraine A. Draper
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland
| | - R Paul Ross
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,Teagasc Food Research Centre, Moorepark, Cork, Ireland
| | - Colin Hill
- APC Microbiome Ireland, University College Cork, Cork, Ireland,School of Microbiology, University College Cork, Cork, Ireland,CONTACT Colin Hill APC Microbiome Ireland & School of Microbiology, University College Cork, Cork, Ireland
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42
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Grishin AV, Karyagina AS, Vasina DV, Vasina IV, Gushchin VA, Lunin VG. Resistance to peptidoglycan-degrading enzymes. Crit Rev Microbiol 2020; 46:703-726. [PMID: 32985279 DOI: 10.1080/1040841x.2020.1825333] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The spread of bacterial strains resistant to commonly used antibiotics urges the development of novel antibacterial compounds. Ideally, these novel antimicrobials should be less prone to the development of resistance. Peptidoglycan-degrading enzymes are a promising class of compounds with a fundamentally different mode of action compared to traditionally used antibiotics. The difference in the mechanism of action implies differences both in the mechanisms of resistance and the chances of its emergence. To critically assess the potential of resistance development to peptidoglycan-degrading enzymes, we review the available evidence for the development of resistance to these enzymes in vitro, along with the known mechanisms of resistance to lysozyme, bacteriocins, autolysins, and phage endolysins. We conclude that genetic determinants of resistance to peptidoglycan-degrading enzymes are unlikely to readily emerge de novo. However, resistance to these enzymes would probably spread by the horizontal transfer between intrinsically resistant and susceptible species. Finally, we speculate that the higher cost of the therapeutics based on peptidoglycan degrading enzymes compared to classical antibiotics might result in less misuse, which in turn would lead to lower selective pressure, making these antibacterials less prone to resistance development.
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Affiliation(s)
- Alexander V Grishin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
| | - Anna S Karyagina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia.,A.N. Belozersky Institute of Physical and Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Daria V Vasina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,A.N. Bach Institute of Biochemistry, Research Center of Biotechnology of the Russian Academy of Sciences, Moscow, Russia
| | - Irina V Vasina
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vladimir A Gushchin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,Faculty of Biology, M.V. Lomonosov Moscow State University, Moscow, Russia
| | - Vladimir G Lunin
- N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, Russia
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43
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Bacteriophage-Derived Endolysins Applied as Potent Biocontrol Agents to Enhance Food Safety. Microorganisms 2020; 8:microorganisms8050724. [PMID: 32413991 PMCID: PMC7285104 DOI: 10.3390/microorganisms8050724] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/11/2020] [Accepted: 05/12/2020] [Indexed: 02/04/2023] Open
Abstract
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.
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Röhrig C, Huemer M, Lorgé D, Luterbacher S, Phothaworn P, Schefer C, Sobieraj AM, Zinsli LV, Mairpady Shambat S, Leimer N, Keller AP, Eichenseher F, Shen Y, Korbsrisate S, Zinkernagel AS, Loessner MJ, Schmelcher M. Targeting Hidden Pathogens: Cell-Penetrating Enzybiotics Eradicate Intracellular Drug-Resistant Staphylococcus aureus. mBio 2020; 11:e00209-20. [PMID: 32291298 PMCID: PMC7157818 DOI: 10.1128/mbio.00209-20] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 03/17/2020] [Indexed: 01/21/2023] Open
Abstract
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.
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Affiliation(s)
- Christian Röhrig
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Markus Huemer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Dominique Lorgé
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Samuel Luterbacher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Preeda Phothaworn
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | | | - Anna M Sobieraj
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Léa V Zinsli
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Srikanth Mairpady Shambat
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Nadja Leimer
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Anja P Keller
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Fritz Eichenseher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Yang Shen
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Sunee Korbsrisate
- Department of Immunology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Annelies S Zinkernagel
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Mathias Schmelcher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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Linker Editing of Pneumococcal Lysin ClyJ Conveys Improved Bactericidal Activity. Antimicrob Agents Chemother 2020; 64:AAC.01610-19. [PMID: 31767724 DOI: 10.1128/aac.01610-19] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 11/18/2019] [Indexed: 12/12/2022] Open
Abstract
Streptococcus pneumoniae is a leading human pathogen uniquely characterized by choline moieties on the bacterial surface. Our previous work reported a pneumococcus-specific chimeric lysin, ClyJ, which combines the CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) enzymatically active domain (EAD) from the PlyC lysin and the cell wall binding domain (CBD) from the phage SPSL1 lysin, which imparts choline binding specificity. Here, we demonstrate that the lytic activity of ClyJ can be further improved by editing the linker sequence adjoining the EAD and CBD. Keeping the net charge of the linker constant, we constructed three ClyJ variants containing different lengths of linker sequence. Circular dichroism showed that linker editing has only minor effects on the folding of the EAD and CBD. However, thermodynamic examination combined with biochemical analysis demonstrated that one variant, ClyJ-3, with the shortest linker, displayed improved thermal stability and bactericidal activity, as well as reduced cytotoxicity. In a pneumococcal mouse infection model, ClyJ-3 showed significant protective efficacy compared to that of the ClyJ parental lysin or the Cpl-1 lysin, with 100% survival at a single ClyJ-3 intraperitoneal dose of 100 μg/mouse. Moreover, a ClyJ-3 dose of 2 μg/mouse had the same efficacy as a ClyJ dose of 40 μg/mouse, suggesting a 20-fold improvement in vivo Taking these results together, the present study not only describes a promising pneumococcal lysin with improved potency, i.e., ClyJ-3, but also implies for the first time that the linker sequence plays an important role in determining the activity of a chimeric lysin, providing insight for future lysin engineering studies.
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Construction and characterization of a chimeric lysin ClyV with improved bactericidal activity against Streptococcus agalactiae in vitro and in vivo. Appl Microbiol Biotechnol 2020; 104:1609-1619. [PMID: 31900556 DOI: 10.1007/s00253-019-10325-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 12/06/2019] [Accepted: 12/15/2019] [Indexed: 01/21/2023]
Abstract
The emergence of antibiotic-resistant beta-hemolytic Streptococcus agalactiae strains poses increasing threat to human beings globally. As an attempt to create a novel lysin with improved activity against S. agalactiae, a chimeric lysin, ClyV, was constructed by fusing the enzymatically active domain (EAD) from PlyGBS lysin (GBS180) and the cell wall binding domain (CBD) from PlyV12 lysin (V12CBD). Plate lysis assay combined with lytic kinetic analysis demonstrated that ClyV has improved activity than its parental enzymatic domain GBS180 against multiple streptococci. Biochemical characterization showed that ClyV is active from pH 7 to 10, with the optimum pH of 9, and is stable under NaCl concentration of < 500 mM. In a S. agalactiae infection model, a single intraperitoneally administration of 0.1 mg/mouse of ClyV protected 100% mice, while it was observed that ~ 29% survive in group that received a single dose of 0.1 mg/mouse of GBS180. Moreover, a high dose of 0.8 mg/mouse ClyV did not show any adverse effects to the health or survival rate of the mice. Considering the robust bactericidal activity and good safety profile of ClyV, it represents a potential candidate for the treatment of S. agalactiae infections.
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Gondil VS, Harjai K, Chhibber S. Endolysins as emerging alternative therapeutic agents to counter drug-resistant infections. Int J Antimicrob Agents 2019; 55:105844. [PMID: 31715257 DOI: 10.1016/j.ijantimicag.2019.11.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 08/02/2019] [Accepted: 11/05/2019] [Indexed: 12/19/2022]
Abstract
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.
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Affiliation(s)
- Vijay Singh Gondil
- Department of Microbiology, Basic Medical Sciences, Panjab University, Chandigarh, India
| | - Kusum Harjai
- Department of Microbiology, Basic Medical Sciences, Panjab University, Chandigarh, India
| | - Sanjay Chhibber
- Department of Microbiology, Basic Medical Sciences, Panjab University, Chandigarh, India.
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Shang X, Nelson DC. Contributions of Net Charge on the PlyC Endolysin CHAP Domain. Antibiotics (Basel) 2019; 8:antibiotics8020070. [PMID: 31142020 PMCID: PMC6628322 DOI: 10.3390/antibiotics8020070] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 05/20/2019] [Accepted: 05/25/2019] [Indexed: 12/18/2022] Open
Abstract
Bacteriophage endolysins, enzymes that degrade the bacterial peptidoglycan (PG), have gained an increasing interest as alternative antimicrobial agents, due to their ability to kill antibiotic resistant pathogens efficiently when applied externally as purified proteins. Typical endolysins derived from bacteriophage that infect Gram-positive hosts consist of an N-terminal enzymatically-active domain (EAD) that cleaves covalent bonds in the PG, and a C-terminal cell-binding domain (CBD) that recognizes specific ligands on the surface of the PG. Although CBDs are usually essential for the EADs to access the PG substrate, some EADs possess activity in the absence of CBDs, and a few even display better activity profiles or an extended host spectrum than the full-length endolysin. A current hypothesis suggests a net positive charge on the EAD enables it to reach the negatively charged bacterial surface via ionic interactions in the absence of a CBD. Here, we used the PlyC CHAP domain as a model EAD to further test the hypothesis. We mutated negatively charged surface amino acids of the CHAP domain that are not involved in structured regions to neutral or positively charged amino acids in order to increase the net charge from -3 to a range from +1 to +7. The seven mutant candidates were successfully expressed and purified as soluble proteins. Contrary to the current hypothesis, none of the mutants were more active than wild-type CHAP. Analysis of electrostatic surface potential implies that the surface charge distribution may affect the activity of a positively charged EAD. Thus, we suggest that while charge should continue to be considered for future engineering efforts, it should not be the sole focus of such engineering efforts.
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Affiliation(s)
- Xiaoran Shang
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.
| | - Daniel C Nelson
- Institute for Bioscience and Biotechnology Research, Rockville, MD 20850, USA.
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA.
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ClyJ Is a Novel Pneumococcal Chimeric Lysin with a Cysteine- and Histidine-Dependent Amidohydrolase/Peptidase Catalytic Domain. Antimicrob Agents Chemother 2019; 63:AAC.02043-18. [PMID: 30642930 DOI: 10.1128/aac.02043-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2018] [Accepted: 01/05/2019] [Indexed: 12/14/2022] Open
Abstract
Streptococcus pneumoniae is one of the leading pathogens that cause a variety of mucosal and invasive infections. With the increased emergence of multidrug-resistant S. pneumoniae, new antimicrobials with mechanisms of action different from conventional antibiotics are urgently needed. In this study, we identified a putative lysin (gp20) encoded by the Streptococcus phage SPSL1 using the LytA autolysin as a template. Molecular dissection of gp20 revealed a binding domain (GPB) containing choline-binding repeats (CBRs) that are high specificity for S. pneumoniae By fusing GPB to the CHAP (cysteine, histidine-dependent amidohydrolase/peptidase) catalytic domain of the PlyC lysin, we constructed a novel chimeric lysin, ClyJ, with improved activity to the pneumococcal Cpl-1 lysin. No resistance was observed in S. pneumoniae strains after exposure to incrementally doubling concentrations of ClyJ for 8 continuous days in vitro In a mouse bacteremia model using penicillin G as a control, a single intraperitoneal injection of ClyJ improved the survival rate of lethal S. pneumoniae-infected mice in a dose-dependent manner. Given its high lytic activity and safety profile, ClyJ may represent a promising alternative to combat pneumococcal infections.
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Hjelm LC, Nilvebrant J, Nygren PÅ, Nilsson AS, Seijsing J. Lysis of Staphylococcal Cells by Modular Lysin Domains Linked via a Non-covalent Barnase-Barstar Interaction Bridge. Front Microbiol 2019; 10:558. [PMID: 30967850 PMCID: PMC6439198 DOI: 10.3389/fmicb.2019.00558] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 03/04/2019] [Indexed: 01/21/2023] Open
Abstract
Bacteriophage endolysins and bacterial exolysins are capable of enzymatic degradation of the cell wall peptidoglycan layer and thus show promise as a new class of antimicrobials. Both exolysins and endolysins often consist of different modules, which are responsible for enzymatic functions and cell wall binding, respectively. Individual modules from different endo- or exolysins with different binding and enzymatic activities, can via gene fusion technology be re-combined into novel variants for investigations of arrangements of potential clinical interest. The aim of this study was to investigate if separately produced cell wall binding and enzyme modules could be assembled into a functional lysin via a non-covalent affinity interaction bridge composed of the barnase ribonuclease from Bacillus amyloliquefaciens and its cognate inhibitor barstar, known to form a stable heterodimeric complex. In a proof-of-principle study, using surface plasmon resonance, flow cytometry and turbidity reduction assays, we show that separately produced modules of a lysin cysteine/histidine-dependent amidohydrolase/peptidase (CHAP) from Staphylococcus aureus bacteriophage K endolysin (LysK) fused to barnase and a cell wall binding Src homology 3 domain (SH3b) from the S. simulans exolysin lysostaphin fused to barstar can be non-covalently assembled into a functional lysin showing both cell wall binding and staphylolytic activity. We hypothesize that the described principle for assembly of functional lysins from separate modules through appended hetero-dimerization domains has a potential for investigations of also other combinations of enzymatically active and cell wall binding domains for desired applications.
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Affiliation(s)
- Linnea C Hjelm
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johan Nilvebrant
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Per-Åke Nygren
- Department of Protein Science, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Anders S Nilsson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Johan Seijsing
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
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