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Hong HW, Jang J, Kim YD, Jeong TH, Lee D, Park K, Kim MS, Yoon IS, Song M, Seo MD, Yoon H, Lim D, Myung H. In vitro and in vivo efficacy studies of an engineered endolysin targeting Gram-negative pathogens. Int J Biol Macromol 2025; 302:140463. [PMID: 39884635 DOI: 10.1016/j.ijbiomac.2025.140463] [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: 11/14/2024] [Revised: 01/09/2025] [Accepted: 01/27/2025] [Indexed: 02/01/2025]
Abstract
Endolysins have drawn considerable attention as viable modalities for antibiotic use. The most significant obstacle for Gram-negative targeting endolysins is the presence of the outer membrane barrier. A heterologously expressed endolysin encoded by bacteriophage PBPA90 infecting Pseudomonas aeruginosa exhibited intrinsic antibacterial activity against P. aeruginosa. The antibacterial efficacy was improved by substituting 15 amino acids and by fusing cecropin A to the N-terminus. The resulting engineered endolysin, LNT103, demonstrated strong antibacterial activity, with minimum inhibitory concentrations as low as 4 μg/ml, against various Gram-negative pathogens in addition to P. aeruginosa, including Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, Klebsiella aerogenes, and Enterobacter cloacae. The engineered endolysin rendered both the outer and the inner bacterial membranes permeable. It exhibited a synergistic effect with colistin, and additive effects with carbapenem antibiotics. Bacterial resistance development to LNT103 was none to minimal in vitro. Its in vivo efficacy was verified in bacteremia models of mice infected with A. baumannii. The endolysin led to a resensitization of resistant bacteria to meropenem when used in combination in vivo.
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Affiliation(s)
- Hye-Won Hong
- LyseNTech Co., Ltd., Suite 1002, Innovalley C, 253 Pangyo-Ro, Bundang-Gu, Seongnam, Gyeonggi-Do 13486, Republic of Korea
| | - Jaeyeon Jang
- LyseNTech Co., Ltd., Suite 1002, Innovalley C, 253 Pangyo-Ro, Bundang-Gu, Seongnam, Gyeonggi-Do 13486, Republic of Korea
| | - Young Deuk Kim
- LyseNTech Co., Ltd., Suite 1002, Innovalley C, 253 Pangyo-Ro, Bundang-Gu, Seongnam, Gyeonggi-Do 13486, Republic of Korea
| | - Tae-Hwan Jeong
- LyseNTech Co., Ltd., Suite 1002, Innovalley C, 253 Pangyo-Ro, Bundang-Gu, Seongnam, Gyeonggi-Do 13486, Republic of Korea
| | - Dogeun Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Kyungah Park
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi-Do 16499, Republic of Korea
| | - Min Soo Kim
- LyseNTech Co., Ltd., Suite 1002, Innovalley C, 253 Pangyo-Ro, Bundang-Gu, Seongnam, Gyeonggi-Do 13486, Republic of Korea
| | - In-Soo Yoon
- Department of Manufacturing Pharmacy, College of Pharmacy and Research Institute for Drug Development, College of Pharmacy, Pusan National University, Busan 46241, Republic of Korea
| | - Miryoung Song
- Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yong-In, Gyeonggi-Do 17035, Republic of Korea
| | - Min-Duk Seo
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi-Do 16499, Republic of Korea; College of Pharmacy, Ajou University, Suwon, Gyeonggi-Do 16499, Republic of Korea
| | - Hyunjin Yoon
- Department of Molecular Science and Technology, Ajou University, Suwon, Gyeonggi-Do 16499, Republic of Korea; Advanced College of Bio-convergence Engineering, Ajou University, Suwon, Gyeonggi-Do 16499, South Korea
| | - Daejin Lim
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Heejoon Myung
- LyseNTech Co., Ltd., Suite 1002, Innovalley C, 253 Pangyo-Ro, Bundang-Gu, Seongnam, Gyeonggi-Do 13486, Republic of Korea; Department of Bioscience and Biotechnology, Hankuk University of Foreign Studies, Yong-In, Gyeonggi-Do 17035, Republic of Korea; The Bacteriophage Bank of Korea, Suite 1002, Innovalley C, 253 Pangyo-Ro, Bundang-Gu, Seongnam, Gyeonggi-Do 13486, Republic of Korea.
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2
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Gittrich MR, Sanderson CM, Wainaina JM, Noel CM, Leopold JE, Babusci E, Selbes SC, Farinas OR, Caine J, Davis II J, Mutalik VK, Hyman P, Sullivan MB. Isolation and characterization of 24 phages infecting the plant growth-promoting rhizobacterium Klebsiella sp. M5al. PLoS One 2025; 20:e0313947. [PMID: 39982899 PMCID: PMC11845039 DOI: 10.1371/journal.pone.0313947] [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: 06/18/2024] [Accepted: 11/03/2024] [Indexed: 02/23/2025] Open
Abstract
Bacteriophages largely impact bacterial communities via lysis, gene transfer, and metabolic reprogramming and thus are increasingly thought to alter nutrient and energy cycling across many of Earth's ecosystems. However, there are few model systems to mechanistically and quantitatively study phage-bacteria interactions, especially in soil systems. Here, we isolated, sequenced, and genomically characterized 24 novel phages infecting Klebsiella sp. M5al, a plant growth-promoting, nonencapsulated rhizosphere-associated bacterium, and compared many of their features against all 565 sequenced, dsDNA Klebsiella phage genomes. Taxonomic analyses revealed that these Klebsiella phages belong to three known phage families (Autographiviridae, Drexlerviridae, and Straboviridae) and two newly proposed phage families (Candidatus Mavericviridae and Ca. Rivulusviridae). At the phage family level, we found that core genes were often phage-centric proteins, such as structural proteins for the phage head and tail and DNA packaging proteins. In contrast, genes involved in transcription, translation, or hypothetical proteins were commonly not shared or flexible genes. Ecologically, we assessed the phages' ubiquity in recent large-scale metagenomic datasets, which revealed they were not widespread, as well as a possible direct role in reprogramming specific metabolisms during infection by screening their genomes for phage-encoded auxiliary metabolic genes (AMGs). Even though AMGs are common in the environmental literature, only one of our phage families, Straboviridae, contained AMGs, and the types of AMGs were correlated at the genus level. Host range phenotyping revealed the phages had a wide range of infectivity, infecting between 1-14 of our 22 bacterial strain panel that included pathogenic Klebsiella and Raoultella strains. This indicates that not all capsule-independent Klebsiella phages have broad host ranges. Together, these isolates, with corresponding genome, AMG, and host range analyses, help build the Klebsiella model system for studying phage-host interactions of rhizosphere-associated bacteria.
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Affiliation(s)
- Marissa R. Gittrich
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, United States of America
| | - Courtney M. Sanderson
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, United States of America
| | - James M. Wainaina
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, United States of America
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, United States of America
| | - Cara M. Noel
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Jonathan E. Leopold
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Erica Babusci
- School of the Environment and Natural Resources, The Ohio State University, Columbus, Ohio, United States of America
| | - Sumeyra C. Selbes
- Department of Psychology, The Ohio State University, Columbus, Ohio, United States of America
| | - Olivia R. Farinas
- College of Public Health, Division of Environmental Health Sciences, The Ohio State University, Columbus, Ohio, United States of America
| | - Jack Caine
- Department of Biology, Kenyon College, Gambier, Ohio, United States of America
| | - Joshua Davis II
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
| | - Vivek K. Mutalik
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Paul Hyman
- Department of Biology/Toxicology, Ashland University, Ashland, Ohio, United States of America
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, Columbus, Ohio, United States of America
- Center of Microbiome Science, The Ohio State University, Columbus, Ohio, United States of America
- Department of Civil, Environmental, and Geodetic Engineering, The Ohio State University, Columbus, Ohio, United States of America
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3
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Kuc-Ciepluch D, Ciepluch K, Augustyniak D, Guła G, Maciejewska B, Kowalik A, Jop E, Drulis-Kawa Z, Arabski M. Exploiting gasdermin-mediated pyroptosis for enhanced antimicrobial activity of phage endolysin against Pseudomonas aeruginosa. mSystems 2025; 10:e0110624. [PMID: 39714210 PMCID: PMC11748493 DOI: 10.1128/msystems.01106-24] [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: 08/14/2024] [Accepted: 12/02/2024] [Indexed: 12/24/2024] Open
Abstract
Pyroptosis is an inflammatory immune response of eukaryotic cells to bacterial lipopolysaccharide (LPS) and other pathological stimuli, leading to the activation of the gasdermin D (GSDMD) and secretion of pore-forming domain GSDMDNterm, facilitating the release of cytokines. Additionally, GSDMDNterm exhibits antibacterial properties through interactions with bacterial outer membranes (OM). We explored alternative antimicrobial strategy to determine whether inducing natural pyroptosis via GSDMD activation by P. aeruginosa LPS could enhance the effectiveness of recombinant phage endopeptidase KP27 (peptidoglycan-degrading enzyme) against P. aeruginosa, enabling penetration through OM and bacterial killing synergistically. Our findings demonstrated that recombinant GSDMD alone exhibited antibacterial effects against wild-type P. aeruginosa with smooth LPS, while recombinant GSDMDNterm efficiently permeabilized both smooth LPS-bearing and O-chain-deficient P. aeruginosa potentially synergizing with endolysin KP27. Transcriptomic analyses revealed the activation of the immune system pathways in response to LPS, mainly in monocytic cells, in contrast to epithelial A549 or HeLa cell lines. LPS-induced pyroptosis in monocytes led to GSDMD cleavage and the release of interleukins, regardless of the nature/origin of the LPS used. However, the pyroptosis stimulation by LPS in the antibacterial assay was not effective enough for bacterial OM permeabilization and enhancement of endolysin activity. We assume that leveraging pyroptosis induction in monocytic cells to augment the bactericidal activity of endolysins may be limited. IMPORTANCE Recombinant GSDMDNterm protein was able to efficiently permeabilize P. aeruginosa outer membranes and increase endolysin activity against bacteria, producing either long LPS O-chains or lack them entirely. The obtained results suggest the limited possibility of using the natural process of pyroptosis occurring in monocytic cells to enhance the bactericidal effect of recombinant phage endolysins against Gram-negative bacteria infection.
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Affiliation(s)
- Dorota Kuc-Ciepluch
- Division of Medical Biology, Jan Kochanowski University in Kielce, Kielce, Poland
| | - Karol Ciepluch
- Division of Medical Biology, Jan Kochanowski University in Kielce, Kielce, Poland
| | - Daria Augustyniak
- Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
| | - Grzegorz Guła
- Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
| | - Artur Kowalik
- Division of Medical Biology, Jan Kochanowski University in Kielce, Kielce, Poland
- Department of Molecular Diagnostics, Holy Cross Cancer Centre, Kielce, Poland
| | - Ewelina Jop
- Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
| | - Michał Arabski
- Division of Medical Biology, Jan Kochanowski University in Kielce, Kielce, Poland
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4
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Zhang P, Zeng P, Lai CKC, Ip M, To KKW, Zuo Z, Xia J, Leung SSY. Synergism of colistin and globular endolysins against multidrug-resistant gram-negative bacteria. Int J Biol Macromol 2024; 278:134670. [PMID: 39151868 DOI: 10.1016/j.ijbiomac.2024.134670] [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: 02/09/2024] [Revised: 08/04/2024] [Accepted: 08/09/2024] [Indexed: 08/19/2024]
Abstract
Endolysins (lysins), a novel class of antibacterial agents derived from bacteriophages, efficiently lyse bacteria by degrading the peptidoglycan layer within the bacterial wall. Colistin, a classic peptide antibiotic with the ability to permeabilize the outer membrane, has recently shown great promise in synergizing with lysins against gram-negative bacteria. However, the exact mechanisms responsible for their synergy remain unclear. Here, we first demonstrated the synergistic bacterial killing of various lysin and colistin combinations. With a model lysin, LysAB2, we then confirmed that there is a threshold concentration of colistin causing sufficient permeabilization of the outer membrane for lysin to access the peptidoglycan layer and subsequently exert its lytic ability. The threshold colistin concentrations were found to range 0.2-0.8 μM for the tested bacteria, with the exact value largely depending on the density of lipopolysaccharides on the outer membrane. Beyond the threshold colistin level, LysAB2 could synergize with colistin at a concentration as low as 0.31 μM. Next, we proved for the first time that lysin-induced degradation of the peptidoglycan layer facilitated the disruption of cytoplasmic membrane by colistin, elevated the level of reactive oxygen species in bacterial cells, and boosted the killing effect of colistin. Additionally, the colistin-lysin combination could effectively eliminate established biofilms due to the biofilm dispersal ability of lysin. The in-vivo efficacy was preliminary confirmed in a Galleria mellonella infection model for combination with colistin doses (≥ 1.8 μg/larvae), which could reach beyond the threshold concentration, and a fixed LysAB2 dose (10 μg/larvae). In summary, our study provided the first experimental evidence unravelling the mechanisms behind the synergy of colistin and lysins. All these findings provided important insights in guiding the dosing strategy for applying this combination in future development.
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Affiliation(s)
- Pengfei Zhang
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Ping Zeng
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Christopher K C Lai
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Zhong Zuo
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Hong Kong.
| | - Sharon S Y Leung
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong.
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5
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Fu Y, Yu S, Li J, Lao Z, Yang X, Lin Z. DeepMineLys: Deep mining of phage lysins from human microbiome. Cell Rep 2024; 43:114583. [PMID: 39110597 DOI: 10.1016/j.celrep.2024.114583] [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: 11/07/2023] [Revised: 06/21/2024] [Accepted: 07/19/2024] [Indexed: 09/01/2024] Open
Abstract
Vast shotgun metagenomics data remain an underutilized resource for novel enzymes. Artificial intelligence (AI) has increasingly been applied to protein mining, but its conventional performance evaluation is interpolative in nature, and these trained models often struggle to extrapolate effectively when challenged with unknown data. In this study, we present a framework (DeepMineLys [deep mining of phage lysins from human microbiome]) based on the convolutional neural network (CNN) to identify phage lysins from three human microbiome datasets. When validated with an independent dataset, our method achieved an F1-score of 84.00%, surpassing existing methods by 20.84%. We expressed 16 lysin candidates from the top 100 sequences in E. coli, confirming 11 as active. The best one displayed an activity 6.2-fold that of lysozyme derived from hen egg white, establishing it as the most potent lysin from the human microbiome. Our study also underscores several important issues when applying AI to biology questions. This framework should be applicable for mining other proteins.
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Affiliation(s)
- Yiran Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Shuting Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Jianfeng Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Zisha Lao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
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6
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Javid M, Shahverdi AR, Ghasemi A, Moosavi-Movahedi AA, Ebrahim-Habibi A, Sepehrizadeh Z. Decoding the Structure-Function Relationship of the Muramidase Domain in E. coli O157.H7 Bacteriophage Endolysin: A Potential Building Block for Chimeric Enzybiotics. Protein J 2024; 43:522-543. [PMID: 38662183 DOI: 10.1007/s10930-024-10195-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: 03/23/2024] [Indexed: 04/26/2024]
Abstract
Bacteriophage endolysins are potential alternatives to conventional antibiotics for treating multidrug-resistant gram-negative bacterial infections. However, their structure-function relationships are poorly understood, hindering their optimization and application. In this study, we focused on the individual functionality of the C-terminal muramidase domain of Gp127, a modular endolysin from E. coli O157:H7 bacteriophage PhaxI. This domain is responsible for the enzymatic activity, whereas the N-terminal domain binds to the bacterial cell wall. Through protein modeling, docking experiments, and molecular dynamics simulations, we investigated the activity, stability, and interactions of the isolated C-terminal domain with its ligand. We also assessed its expression, solubility, toxicity, and lytic activity using the experimental data. Our results revealed that the C-terminal domain exhibits high activity and toxicity when tested individually, and its expression is regulated in different hosts to prevent self-destruction. Furthermore, we validated the muralytic activity of the purified refolded protein by zymography and standardized assays. These findings challenge the need for the N-terminal binding domain to arrange the active site and adjust the gap between crucial residues for peptidoglycan cleavage. Our study shed light on the three-dimensional structure and functionality of muramidase endolysins, thereby enriching the existing knowledge pool and laying a foundation for accurate in silico modeling and the informed design of next-generation enzybiotic treatments.
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Affiliation(s)
- Mehri Javid
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Reza Shahverdi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Azadeh Ebrahim-Habibi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Zargham Sepehrizadeh
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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7
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Espaillat A, Alvarez L, Torrens G, Ter Beek J, Miguel-Ruano V, Irazoki O, Gago F, Hermoso JA, Berntsson RPA, Cava F. A distinctive family of L,D-transpeptidases catalyzing L-Ala-mDAP crosslinks in Alpha- and Betaproteobacteria. Nat Commun 2024; 15:1343. [PMID: 38351082 PMCID: PMC10864386 DOI: 10.1038/s41467-024-45620-5] [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: 11/09/2023] [Accepted: 01/29/2024] [Indexed: 02/16/2024] Open
Abstract
The bacterial cell-wall peptidoglycan is made of glycan strands crosslinked by short peptide stems. Crosslinks are catalyzed by DD-transpeptidases (4,3-crosslinks) and LD-transpeptidases (3,3-crosslinks). However, recent research on non-model species has revealed novel crosslink types, suggesting the existence of uncharacterized enzymes. Here, we identify an LD-transpeptidase, LDTGo, that generates 1,3-crosslinks in the acetic-acid bacterium Gluconobacter oxydans. LDTGo-like proteins are found in Alpha- and Betaproteobacteria lacking LD3,3-transpeptidases. In contrast with the strict specificity of typical LD- and DD-transpeptidases, LDTGo can use non-terminal amino acid moieties for crosslinking. A high-resolution crystal structure of LDTGo reveals unique features when compared to LD3,3-transpeptidases, including a proline-rich region that appears to limit substrate access, and a cavity accommodating both glycan chain and peptide stem from donor muropeptides. Finally, we show that DD-crosslink turnover is involved in supplying the necessary substrate for LD1,3-transpeptidation. This phenomenon underscores the interplay between distinct crosslinking mechanisms in maintaining cell wall integrity in G. oxydans.
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Affiliation(s)
- Akbar Espaillat
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
- Chr. Hansen A/S, Microbial Physiology, R&D, 2970, Hoersholm, Denmark
| | - Laura Alvarez
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Gabriel Torrens
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Josy Ter Beek
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Vega Miguel-Ruano
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Blas Cabrera", CSIC, Madrid, Spain
| | - Oihane Irazoki
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden
| | - Federico Gago
- Department of Biomedical Sciences & IQM-CSIC Associate Unit, School of Medicine and Health Sciences, University of Alcalá, E-28805, Madrid, Alcalá de Henares, Spain
| | - Juan A Hermoso
- Department of Crystallography and Structural Biology, Institute of Physical Chemistry "Blas Cabrera", CSIC, Madrid, Spain
| | - Ronnie P-A Berntsson
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
- Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden
| | - Felipe Cava
- Department of Molecular Biology and Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, SciLifeLab, Umeå University, Umeå, Sweden.
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8
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Li P, Shen M, Ma W, Zhou X, Shen J. LysZX4-NCA, a new endolysin with broad-spectrum antibacterial activity for topical treatment. Virus Res 2024; 340:199296. [PMID: 38065302 PMCID: PMC10755502 DOI: 10.1016/j.virusres.2023.199296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 12/02/2023] [Accepted: 12/05/2023] [Indexed: 01/01/2024]
Abstract
The prevalence of multidrug-resistant highly virulent Klebsiella pneumoniae (MDR-hvKP) requires the development of new therapeutic agents. Herein, a novel lytic phage vB_KpnS_ZX4 against MDR-hvKP was discovered in hospital sewage. Phage vB_KpnS_ZX4 had a short latent period (5 min) and a large burst size (230 PFU/cell). It can rapidly reduce the number of bacteria in vitro and improve survival rates of bacteremic mice in vivo from 0 to 80 % with a single injection of 108 PFU. LysZX4, an endolysin derived from vB_KpnS_ZX4, exhibits potent antimicrobial activity in vitro in combination with ethylenediaminetetraacetic acid (EDTA). The antimicrobial activity of LysZX4 was further enhanced by the fusion of KWKLFKI residues from cecropin A (LysZX4-NCA). In vitro antibacterial experiments showed that LysZX4-NCA exerts broad-spectrum antibacterial activity against clinical Gram-negative bacteria, including MDR-hvKP. Moreover, in the mouse model of MDR-hvKP skin infection, treatment with LysZX4-NCA resulted in a three-log reduction in bacterial burden on the skin compared to the control group. Therefore, the novel phages vB_KpnS_ZX4 and LysZX4-NCA are effective reagents for the treatment of systemic and local MDR-hvKP infections.
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Affiliation(s)
- Ping Li
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, PR China
| | - Mangmang Shen
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, PR China
| | - Wenjie Ma
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, PR China
| | - Xin Zhou
- College of Veterinary Medicine, Institute of Comparative Medicine, Yangzhou University, Yangzhou 225009, PR China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, PR China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University, Yangzhou 225009, PR China.
| | - Jiayin Shen
- The Third People's Hospital of Shenzhen, Shenzhen 518112, PR China.
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9
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Son SM, Kim J, Ryu S. Development of sensitizer peptide-fused endolysin Lys1S-L9P acting against multidrug-resistant gram-negative bacteria. Front Microbiol 2023; 14:1296796. [PMID: 38075915 PMCID: PMC10701683 DOI: 10.3389/fmicb.2023.1296796] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 11/01/2023] [Indexed: 06/21/2024] Open
Abstract
The advent of multidrug-resistant (MDR) bacteria poses a major threat to public health, garnering attention to novel antibiotic replacements. Endolysin, a bacteriophage-derived cell wall-degrading enzyme, is a promising alternative to conventional antibiotics. However, it is challenging to control Gram-negative bacteria due to the presence of the outer membrane that shields the peptidoglycan layer from enzymatic degradation. To overcome this threshold, we constructed the fusion endolysin Lys1S-L9P by combining endolysin LysSPN1S with KL-L9P, a sensitizer peptide known to extend efficacy of antibiotics by perturbing the outer membrane of Gram-negative bacteria. In addition, we established a new endolysin purification procedure that increases solubility allowing a 4-fold increase in production yield of Lys1S-L9P. The sensitizer peptide-fused endolysin Lys1S-L9P exhibited high bactericidal effects against many MDR Gram-negative pathogens and was more effective in eradicating biofilms compared to LysSPN1S. Moreover, Lys1S-L9P showed potential for clinical use, maintaining stability at various storage temperatures without cytotoxicity against human cells. In the in vivo Galleria mellonella model, Lys1S-L9P demonstrated potent antibacterial activity against MDR Gram-negative bacteria without inducing any toxic activity. This study suggest that Lys1S-L9P could be a potential biocontrol agent to combat MDR Gram-negative bacteria.
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Affiliation(s)
- Su Min Son
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
| | - Joonbeom Kim
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
| | - Sangryeol Ryu
- Department of Food and Animal Biotechnology, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea
- Department of Agricultural Biotechnology, Seoul National University, Seoul, Republic of Korea
- Center for Food and Bioconvergence, Seoul National University, Seoul, Republic of Korea
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10
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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: 4] [Impact Index Per Article: 2.0] [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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11
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Shah S, Das R, Chavan B, Bajpai U, Hanif S, Ahmed S. Beyond antibiotics: phage-encoded lysins against Gram-negative pathogens. Front Microbiol 2023; 14:1170418. [PMID: 37789862 PMCID: PMC10542408 DOI: 10.3389/fmicb.2023.1170418] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Accepted: 08/25/2023] [Indexed: 10/05/2023] Open
Abstract
Antibiotics remain the frontline agents for treating deadly bacterial pathogens. However, the indiscriminate use of these valuable agents has led to an alarming rise in AMR. The antibiotic pipeline is insufficient to tackle the AMR threat, especially with respect to the WHO critical category of priority Gram-negative pathogens, which have become a serious problem as nosocomial and community infections and pose a threat globally. The AMR pandemic requires solutions that provide novel antibacterial agents that are not only effective but against which bacteria are less likely to gain resistance. In this regard, natural or engineered phage-encoded lysins (enzybiotics) armed with numerous features represent an attractive alternative to the currently available antibiotics. Several lysins have exhibited promising efficacy and safety against Gram-positive pathogens, with some in late stages of clinical development and some commercially available. However, in the case of Gram-negative bacteria, the outer membrane acts as a formidable barrier; hence, lysins are often used in combination with OMPs or engineered to overcome the outer membrane barrier. In this review, we have briefly explained AMR and the initiatives taken by different organizations globally to tackle the AMR threat at different levels. We bring forth the promising potential and challenges of lysins, focusing on the WHO critical category of priority Gram-negative bacteria and lysins under investigation for these pathogens, along with the challenges associated with developing them as therapeutics within the existing regulatory framework.
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Affiliation(s)
- Sanket Shah
- Techinvention Lifecare Private Limited, Mumbai, India
| | - Ritam Das
- Techinvention Lifecare Private Limited, Mumbai, India
| | - Bhakti Chavan
- Techinvention Lifecare Private Limited, Mumbai, India
| | - Urmi Bajpai
- Department of Biomedical Science, Acharya Narendra Dev College, University of Delhi, New Delhi, India
| | - Sarmad Hanif
- Techinvention Lifecare Private Limited, Mumbai, India
| | - Syed Ahmed
- Techinvention Lifecare Private Limited, Mumbai, India
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12
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Mikoulinskaia GV, Prokhorov DA, Chernyshov SV, Sitnikova DS, Arakelian AG, Uversky VN. Conservative Tryptophan Residue in the Vicinity of an Active Site of the M15 Family l,d-Peptidases: A Key Element in the Catalysis. Int J Mol Sci 2023; 24:13249. [PMID: 37686055 PMCID: PMC10487532 DOI: 10.3390/ijms241713249] [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: 07/27/2023] [Revised: 08/22/2023] [Accepted: 08/25/2023] [Indexed: 09/10/2023] Open
Abstract
Bioinformatics analysis of the sequences of orthologous zinc-containing peptidases of the M15_C subfamily revealed the presence of a conserved tryptophan residue near the active site, which is not involved in the formation of the protein core. Site-directed mutagenesis of this Trp114/109 residue using two representatives of the family, l-alanoyl-d-glutamate peptidases of bacteriophages T5 (calcium-activated EndoT5) and RB49 (EndoRB49, without ion regulation) as examples, and further analysis of the 1H NMR spectra of the mutants showed that a decrease in the volume of the W → F → A residue leads to changes in the hydrophobic core and active center of the protein, and also decreases the affinity for regulatory Ca2+ in the EndoT5 mutants. The inactive T5W114A mutant lacks the ability to bind the substrate. In general, the conserved Trp114/109 residue, due to the spatial restrictions of its side chain, significantly affects the formation of the catalytically active form of the enzyme and is critical for catalysis.
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Affiliation(s)
- Galina V. Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry, RAS, Prospekt Nauki, 6, 142290 Pushchino, Moscow Region, Russia; (S.V.C.); (D.S.S.); (A.G.A.)
| | - Dmitry A. Prokhorov
- Institute of Theoretical and Experimental Biophysics, RAS, Institutskaya ul., 3, 142290 Pushchino, Moscow Region, Russia;
| | - Sergei V. Chernyshov
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry, RAS, Prospekt Nauki, 6, 142290 Pushchino, Moscow Region, Russia; (S.V.C.); (D.S.S.); (A.G.A.)
| | - Daria S. Sitnikova
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry, RAS, Prospekt Nauki, 6, 142290 Pushchino, Moscow Region, Russia; (S.V.C.); (D.S.S.); (A.G.A.)
| | - Arina G. Arakelian
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry, RAS, Prospekt Nauki, 6, 142290 Pushchino, Moscow Region, Russia; (S.V.C.); (D.S.S.); (A.G.A.)
- Institute of Theoretical and Experimental Biophysics, RAS, Institutskaya ul., 3, 142290 Pushchino, Moscow Region, Russia;
| | - Vladimir N. Uversky
- Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, 142290 Pushchino, Moscow Region, Russia
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
- USF Health Byrd Alzheimer’s Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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13
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Lourenço M, Osbelt L, Passet V, Gravey F, Megrian D, Strowig T, Rodrigues C, Brisse S. Phages against Noncapsulated Klebsiella pneumoniae: Broader Host range, Slower Resistance. Microbiol Spectr 2023; 11:e0481222. [PMID: 37338376 PMCID: PMC10433977 DOI: 10.1128/spectrum.04812-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 05/23/2023] [Indexed: 06/21/2023] Open
Abstract
Klebsiella pneumoniae (Kp), a human gut colonizer and opportunistic pathogen, is a major contributor to the global burden of antimicrobial resistance. Virulent bacteriophages represent promising agents for decolonization and therapy. However, the majority of anti-Kp phages that have been isolated thus far are highly specific to unique capsular types (anti-K phages), which is a major limitation to phage therapy prospects due to the highly polymorphic capsule of Kp. Here, we report on an original anti-Kp phage isolation strategy, using capsule-deficient Kp mutants as hosts (anti-Kd phages). We show that anti-Kd phages have a broad host range, as the majority are able to infect noncapsulated mutants of multiple genetic sublineages and O-types. Additionally, anti-Kd phages induce a lower rate of resistance emergence in vitro and provide increased killing efficiency when in combination with anti-K phages. In vivo, anti-Kd phages are able to replicate in mouse guts colonized with a capsulated Kp strain, suggesting the presence of noncapsulated Kp subpopulations. The original strategy proposed here represents a promising avenue that circumvents the Kp capsule host restriction barrier, offering promise for therapeutic development. IMPORTANCE Klebsiella pneumoniae (Kp) is an ecologically generalist bacterium as well as an opportunistic pathogen that is responsible for hospital-acquired infections and a major contributor to the global burden of antimicrobial resistance. In the last decades, limited advances have been made in the use of virulent phages as alternatives or complements to antibiotics that are used to treat Kp infections. This work demonstrates the potential value of an anti-Klebsiella phage isolation strategy that addresses the issue of the narrow host range of anti-K phages. Anti-Kd phages may be active in infection sites in which capsule expression is intermittent or repressed or in combination with anti-K phages, which often induce the loss of capsule in escape mutants.
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Affiliation(s)
- Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Virginie Passet
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - François Gravey
- Dynamycure Inserm UM1311 Normandie Univ, UNICAEN, UNIROUEN, Caen, France
| | - Daniela Megrian
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Carla Rodrigues
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
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14
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Mohammadi M, Saffari M, Siadat SD. Phage therapy of antibiotic-resistant strains of Klebsiella pneumoniae, opportunities and challenges from the past to the future. Folia Microbiol (Praha) 2023; 68:357-368. [PMID: 37036571 DOI: 10.1007/s12223-023-01046-y] [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: 10/07/2022] [Accepted: 03/12/2023] [Indexed: 04/11/2023]
Abstract
Klebsiella spp. is a commensal gram-negative bacterium and a member of the human microbiota. It is the leading cause of various hospital-acquired infections. The occurrence of multi-drug drug resistance and carbapenemase-producing strains of Klebsiella pneumoniae producing weighty contaminations is growing, and Klebsiella oxytoca is an arising bacterium. Alternative approaches to tackle contaminations led by these microorganisms are necessary as strains enhance opposing to last-stage antibiotics in the way that Colistin. The lytic bacteriophages are viruses that infect and rapidly eradicate bacterial cells and are strain-specific to their hosts. They and their proteins are immediately deliberate as opportunities or adjuncts to antibiotic therapy. There are several reports in vitro and in vivo form that proved the potential use of lytic phages to combat superbug stains of K. pneumoniae. Various reports dedicated that the phage area can be returned to the elimination of multi-drug resistance and carbapenemase resistance isolates of K. pneumoniae. This review compiles our current information on phages of Klebsiella spp. and highlights technological and biological issues related to the evolution of phage-based therapies targeting these bacterial hosts.
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Affiliation(s)
- Mehrdad Mohammadi
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran.
| | - Mahmood Saffari
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Kashan, Iran
| | - Seyed Davar Siadat
- Tuberculosis and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran
- Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
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15
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Euler CW, Raz A, Hernandez A, Serrano A, Xu S, Andersson M, Zou G, Zhang Y, Fischetti VA, Li J. PlyKp104, a Novel Phage Lysin for the Treatment of Klebsiella pneumoniae, Pseudomonas aeruginosa, and Other Gram-Negative ESKAPE Pathogens. Antimicrob Agents Chemother 2023; 67:e0151922. [PMID: 37098944 PMCID: PMC10190635 DOI: 10.1128/aac.01519-22] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 03/30/2023] [Indexed: 04/27/2023] Open
Abstract
Klebsiella pneumoniae and Pseudomonas aeruginosa are two leading causes of burn and wound infections, pneumonia, urinary tract infections, and more severe invasive diseases, which are often multidrug resistant (MDR) or extensively drug resistant. Due to this, it is critical to discover alternative antimicrobials, such as bacteriophage lysins, against these pathogens. Unfortunately, most lysins that target Gram-negative bacteria require additional modifications or outer membrane permeabilizing agents to be bactericidal. We identified four putative lysins through bioinformatic analysis of Pseudomonas and Klebsiella phage genomes in the NCBI database and then expressed and tested their intrinsic lytic activity in vitro. The most active lysin, PlyKp104, exhibited >5-log killing against K. pneumoniae, P. aeruginosa, and other Gram-negative representatives of the multidrug-resistant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, K. pneumonia, Acinetobacter baumannii, P. aeruginosa, and Enterobacter species) without further modification. PlyKp104 displayed rapid killing and high activity over a wide pH range and in high concentrations of salt and urea. Additionally, pulmonary surfactants and low concentrations of human serum did not inhibit PlyKp104 activity in vitro. PlyKp104 also significantly reduced drug-resistant K. pneumoniae >2 logs in a murine skin infection model after one treatment of the wound, suggesting that this lysin could be used as a topical antimicrobial against K. pneumoniae and other MDR Gram-negative infections.
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Affiliation(s)
- Chad W. Euler
- State Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, New York, USA
- Department of Medical Laboratory Sciences, Hunter College, CUNY, New York, New York, USA
- Department of Microbiology and Immunology, Weill Cornell Medical College, New York, New York, USA
| | - Assaf Raz
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, New York, USA
- Department of Medical Laboratory Sciences, Hunter College, CUNY, New York, New York, USA
| | - Anaise Hernandez
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, New York, USA
- Department of Medical Laboratory Sciences, Hunter College, CUNY, New York, New York, USA
| | - Anna Serrano
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, New York, USA
| | - Siyue Xu
- State Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, New York, USA
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Martin Andersson
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, New York, USA
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Geng Zou
- State Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Yue Zhang
- State Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Vincent A. Fischetti
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, New York, USA
| | - Jinquan Li
- State Key Laboratory of Agricultural Microbiology, College of Biomedicine and Health, College of Food Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Laboratory of Bacterial Pathogenesis and Immunology, The Rockefeller University, New York, New York, USA
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16
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Pertics BZ, Kovács T, Schneider G. Characterization of a Lytic Bacteriophage and Demonstration of Its Combined Lytic Effect with a K2 Depolymerase on the Hypervirulent Klebsiella pneumoniae Strain 52145. Microorganisms 2023; 11:microorganisms11030669. [PMID: 36985241 PMCID: PMC10051899 DOI: 10.3390/microorganisms11030669] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Klebsiella pneumoniae is a nosocomial pathogen. Among its virulence factors is the capsule with a prominent role in defense and biofilm formation. Bacteriophages (phages) can evoke the lysis of bacterial cells. Due to the mode of action of their polysaccharide depolymerase enzymes, phages are typically specific for one bacterial strain and its capsule type. In this study, we characterized a bacteriophage against the capsule-defective mutant of the nosocomial K. pneumoniae 52145 strain, which lacks K2 capsule. The phage showed a relatively narrow host range but evoked lysis on a few strains with capsular serotypes K33, K21, and K24. Phylogenetic analysis showed that the newly isolated Klebsiella phage 731 belongs to the Webervirus genus in the Drexlerviridae family; it has a 31.084 MDa double-stranded, linear DNA with a length of 50,306 base pairs and a G + C content of 50.9%. Out of the 79 open reading frames (ORFs), we performed the identification of orf22, coding for a trimeric tail fiber protein with putative capsule depolymerase activity, along with the mapping of other putative depolymerases of phage 731 and homologous phages. Efficacy of a previously described recombinant K2 depolymerase (B1dep) was tested by co-spotting phage 731 on K. pneumoniae strains, and it was demonstrated that the B1dep-phage 731 combination allows the lysis of the wild type 52145 strain, originally resistant to the phage 731. With phage 731, we showed that B1dep is a promising candidate for use as a possible antimicrobial agent, as it renders the virulent strain defenseless against other phages. Phage 731 alone is also important due to its efficacy on K. pneumoniae strains possessing epidemiologically important serotypes.
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Affiliation(s)
- Botond Zsombor Pertics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti St. 12., H-7624 Pécs, Hungary
| | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Kertváros St. 2., H-7632 Pécs, Hungary
| | - György Schneider
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti St. 12., H-7624 Pécs, Hungary
- Correspondence: ; Tel.: +36-72-536-200 (ext. 1908)
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17
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Baqer AA, Fang K, Mohd-Assaad N, Adnan SNA, Md Nor NS. In Vitro Activity, Stability and Molecular Characterization of Eight Potent Bacteriophages Infecting Carbapenem-Resistant Klebsiella pneumoniae. Viruses 2022; 15:117. [PMID: 36680156 PMCID: PMC9860934 DOI: 10.3390/v15010117] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/20/2022] [Accepted: 12/26/2022] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Members of the genus Klebsiella are among the leading microbial pathogens associated with nosocomial infection. The increased incidence of antimicrobial resistance in these species has propelled the need for alternate/combination therapeutic regimens to aid clinical treatment, including bacteriophage therapy. Bacteriophages are considered very safe and effective in treating bacterial infections. In this study, we characterize eight lytic bacteriophages that were previously isolated by our team against carbapenem-resistant Klebsiella pneumoniae. METHODS The one-step-growth curves, stability and lytic ability of eight bacteriophages were characterized. Restriction fragment length polymorphism (RFLP), random amplification of polymorphic DNA (RAPD) typing analysis and protein profiling were used to characterize the microbes at the molecular level. Phylogenetic trees of four important proteins were constructed for the two selected bacteriophages. RESULTS AND CONCLUSIONS All eight bacteriophages showed high efficiency for reducing bacterial concentration with high stability under different physical and chemical conditions. We found four major protein bands out of at least ten 15-190 KDa bands that were clearly separated by SDS-PAGE, which were assumed to be the major head and tail proteins. The genomes were found to be dsDNA, with sizes of approximately 36-87 Kb. All bacteriophages reduced the optical density of the planktonic K. pneumoniae abruptly, indicating great potential to reduce K. pneumoniae infection. In this study, we have found that tail fiber protein can further distinguished closely related bacteriophages. The characterised bacteriophages showed promising potential as candidates against carbapenem-resistant Klebsiella pneumoniae via bacteriophage therapy.
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Affiliation(s)
- Abeer Ameen Baqer
- Medical Laboratory Techniques Department, Dijlah University College, Baghdad 10021, Iraq;
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi 43600, SGR, Malaysia;
| | - Kokxin Fang
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi 43600, SGR, Malaysia;
| | - Norfarhan Mohd-Assaad
- Department of Applied Physics, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi 43600, SGR, Malaysia;
- Institute for Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, SGR, Malaysia
| | - Siti Noor Adnalizawati Adnan
- Faculty of Dentistry, Universiti Sains Islam Malaysia, Level 15, Tower B, Persiaran MPAJ, Jalan Pandan Utama, Kuala Lumpur 55100, SGR, Malaysia;
| | - Norefrina Shafinaz Md Nor
- Department of Biological Sciences and Biotechnology, Faculty of Science & Technology, Universiti Kebangsaan Malaysia, Bangi 43600, SGR, Malaysia;
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18
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Smith-Zaitlik T, Shibu P, McCartney AL, Foster G, Hoyles L, Negus D. Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36156193 DOI: 10.1099/mic.0.001247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several hypothetical homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Differences in the tail fibre protein may explain the non-identical host range of the two phages. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.
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Affiliation(s)
| | - Preetha Shibu
- Life Sciences, University of Westminster, London, UK.,Present address: Berkshire and Surrey Pathology Services, Frimley Health NHS Trust, Wexham Park Hospital, Slough, UK
| | - Anne L McCartney
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | | | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK
| | - David Negus
- Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK
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19
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PhREEPred: Phage Resistance Emergence Prediction web to foresee encapsulated bacterial escape from phage cocktail treatment. J Mol Biol 2022; 434:167670. [PMID: 35671831 DOI: 10.1016/j.jmb.2022.167670] [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: 02/01/2022] [Revised: 05/06/2022] [Accepted: 06/01/2022] [Indexed: 11/22/2022]
Abstract
Phages, as well as phage-derived proteins, especially lysins and depolymerases, are intensively studied to become prospective alternatives or supportive antibacterials used alone or in combination. In the common phage therapy approach, the unwanted emergence of phage-resistant variants from the treated bacterial population can be postponed or reduced by the utilization of an effective phage cocktail. In this work, we present a publicly available web tool PhREEPred (Phage Resistance Emergence Prediction) (https://phartner.shinyapps.io/PhREEPred/), which will allow an informed choice of the composition of phage cocktails by predicting the outcome of phage cocktail or phage/depolymerase combination treatments given a mutating population that escapes single phage treatment. PhREEPred simulates solutions of our mathematical model calibrated and tested on the experimental Klebsiella pneumoniae setup and Klebsiella-specific lytic phages: K63 type-specific phage KP34 equipped with a capsule-degrading enzyme (KP34p57), capsule-independent myoviruses KP15 and KP27, and recombinant capsule depolymerase KP34p57. The model can calculate the phage-resistance emergence depending on the bacterial growth rate and initial density, the multiplicity of infection, phage latent period, its infectiveness and the cocktail composition, as well as initial depolymerase concentration and activity rate. This model reproduced the experimental results and showed that (i) the phage cocktail of parallelly infecting phages is less effective than the one composed of sequentially infecting phages; (ii) depolymerase can delay or prevent bacterial resistance by unveiling an alternative receptor for initially inactive phages. In our opinion, this customer-friendly web tool will allow for the primary design of the phage cocktail and phage-depolymerase combination effectiveness against encapsulated pathogens.
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Biofunctionalization of Endolysins with Oligosacharides: Formulation of Therapeutic Agents to Combat Multi-Resistant Bacteria and Potential Strategies for Their Application. POLYSACCHARIDES 2022. [DOI: 10.3390/polysaccharides3020018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
In the aquaculture sector, the biofunctionalization of biomaterials is discussed using materials from algae and analyzed as a possible potential strategy to overcome the challenges that hinder the future development of the application of endolysins in this field. Derived from years of analysis, endolysins have recently been considered as potential alternative therapeutic antibacterial agents, due to their attributes and ability to combat multi-resistant bacterial cells when applied externally. On the other hand, although the aquaculture sector has been characterized by its high production rates, serious infectious diseases have led to significant economic losses that persist to this day. Although there are currently interesting data from studies under in vitro conditions on the application of endolysins in this sector, there is little or no information on in vivo studies. This lack of analysis can be attributed to the relatively low stability of endolysins in marine conditions and to the complex gastrointestinal conditions of the organisms. This review provides updated information regarding the application of endolysins against multi-resistant bacteria of clinical and nutritional interest, previously addressing their important characteristics (structure, properties and stability). In addition, regarding the aquaculture sector, the biofunctionalization of biomaterials is discussed using materials from algae and analyzed as a possible potential strategy to overcome the challenges that hinder the future development of the application of endolysins in this field.
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Singh A, Padmesh S, Dwivedi M, Kostova I. How Good are Bacteriophages as an Alternative Therapy to Mitigate Biofilms of Nosocomial Infections. Infect Drug Resist 2022; 15:503-532. [PMID: 35210792 PMCID: PMC8860455 DOI: 10.2147/idr.s348700] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/27/2022] [Indexed: 12/12/2022] Open
Abstract
Bacteria survive on any surface through the generation of biofilms that provide a protective environment to grow as well as making them drug resistant. Extracellular polymeric matrix is a crucial component in biofilm formation. The presence of biofilms consisting of common opportunistic and nosocomial, drug-resistant pathogens has been reported on medical devices like catheters and prosthetics, leading to many complications. Several approaches are under investigation to combat drug-resistant bacteria. Deployment of bacteriophages is one of the promising approaches to invade biofilm that may expose bacteria to the conditions adverse for their growth. Penetration into these biofilms and their destruction by bacteriophages is brought about due to their small size and ability of their progeny to diffuse through the bacterial cell wall. The other mechanisms employed by phages to infect biofilms may include their relocation through water channels to embedded host cells, replication at local sites followed by infection to the neighboring cells and production of depolymerizing enzymes to decompose viscous biofilm matrix, etc. Various research groups are investigating intricacies involved in phage therapy to mitigate the bacterial infection and biofilm formation. Thus, bacteriophages represent a good control over different biofilms and further understanding of phage-biofilm interaction at molecular level may overcome the clinical challenges in phage therapy. The present review summarizes the comprehensive details on dynamic interaction of phages with bacterial biofilms and the role of phage-derived enzymes - endolysin and depolymerases in extenuating biofilms of clinical and medical concern. The methodology employed was an extensive literature search, using several keywords in important scientific databases, such as Scopus, Web of Science, PubMed, ScienceDirect, etc. The keywords were also used with Boolean operator "And". More than 250 relevant and recent articles were selected and reviewed to discuss the evidence-based data on the application of phage therapy with recent updates, and related potential challenges.
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Affiliation(s)
- Aditi Singh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, 226028, India
| | - Sudhakar Padmesh
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, 226028, India
| | - Manish Dwivedi
- Amity Institute of Biotechnology, Amity University Uttar Pradesh, Lucknow Campus, Lucknow, 226028, India
| | - Irena Kostova
- Department of Chemistry, Faculty of Pharmacy, Medical University, Sofia, 1000, Bulgaria
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Marques AT, Tanoeiro L, Duarte A, Gonçalves L, Vítor JMB, Vale FF. Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates. Microorganisms 2021; 9:2252. [PMID: 34835377 PMCID: PMC8617712 DOI: 10.3390/microorganisms9112252] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
Klebsiella pneumoniae is an increasing threat to public health and represents one of the most concerning pathogens involved in life-threatening infections. The resistant and virulence determinants are coded by mobile genetic elements which can easily spread between bacteria populations and co-evolve with its genomic host. In this study, we present the full genomic sequences, insertion sites and phylogenetic analysis of 150 prophages found in 40 K. pneumoniae clinical isolates obtained from an outbreak in a Portuguese hospital. All strains harbored at least one prophage and we identified 104 intact prophages (69.3%). The prophage size ranges from 29.7 to 50.6 kbp, coding between 32 and 78 putative genes. The prophage GC content is 51.2%, lower than the average GC content of 57.1% in K. pneumoniae. Complete prophages were classified into three families in the order Caudolovirales: Myoviridae (59.6%), Siphoviridae (38.5%) and Podoviridae (1.9%). In addition, an alignment and phylogenetic analysis revealed nine distinct clusters. Evidence of recombination was detected within the genome of some prophages but, in most cases, proteins involved in viral structure, transcription, replication and regulation (lysogenic/lysis) were maintained. These results support the knowledge that prophages are diverse and widely disseminated in K. pneumoniae genomes, contributing to the evolution of this species and conferring additional phenotypes. Moreover, we identified K. pneumoniae prophages in a set of endolysin genes, which were found to code for proteins with lysozyme activity, cleaving the β-1,4 linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in the peptidoglycan network and thus representing genes with the potential for lysin phage therapy.
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Affiliation(s)
- Andreia T. Marques
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (J.M.B.V.)
| | - Luís Tanoeiro
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (J.M.B.V.)
| | - Aida Duarte
- Faculty of Pharmacy, Universidade de Lisboa, Av. Gama Pinto, 1649-003 Lisboa, Portugal;
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, 2829-511 Monte da Caparica, Portugal
| | - Luisa Gonçalves
- Clinical Pathology Unit, Hospital SAMS, Cidade de Gabela, 1849-017 Lisboa, Portugal;
| | - Jorge M. B. Vítor
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (J.M.B.V.)
| | - Filipa F. Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (J.M.B.V.)
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Torabi LR, Naghavi NS, Doudi M, Monajemi R. Efficacious antibacterial potency of novel bacteriophages against ESBL-producing Klebsiella pneumoniae isolated from burn wound infections. IRANIAN JOURNAL OF MICROBIOLOGY 2021; 13:678-690. [PMID: 34900166 PMCID: PMC8629815 DOI: 10.18502/ijm.v13i5.7435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
BACKGROUND AND OBJECTIVES Prevalence of extended spectrum β-lactamase (ESBL) leads to the development of antibiotic resistance and mortality in burn patients. One of the alternative strategies for controlling ESBL bacterial infections is clinical trials of bacteriophage therapy. The aim of this study was to isolate and characterize specific bacteriophages against ESBL-producing Klebsiella pneumoniae in patients with burn ulcers. MATERIALS AND METHODS Clinical samples were isolated from the hospitalized patient in burn medical centers, Iran. Biochemical screenings and 16S rRNA gene sequencing were determined. The phages were isolated from municipal sewerage treatment plants, Isfahan, Iran. TEM and FESEM, adsorption velocity, growth curve, host range, and the viability of the phage particles as well as proteomics and enzyme digestion patterns were examined. RESULTS The results showed that Klebsiella pneumoniae Iaufa_lad2 (GenBank accession number: MW836954) was confirmed as an ESBL-producing strain using combined disk method. This bacterium showed significant sensitivity to three phages including PɸBw-Kp1, PɸBw-Kp2, and PɸBw-Kp3. Morphological characterization demonstrated that the phage PɸBw-Kp3 to the Siphoviridae family (lambda-like phages) and both phages PɸBw-Kp1 and ɸBw-Kp2 to the Podoviridae family (T1-like phages). The isolated bacteriophages had a large burst size, thermal and pH viability and efficient adsorption rate to the host cells. CONCLUSION In present study, the efficacy of bacteriophages against ESBL pathogenic bacterium promises a remarkable achievement for phage therapy. It seems that, these isolated bacteriophages, in the form of phage cocktails, had a strong antibacterial impacts and a broad-spectrum strategy against ESBL-producing Klebsiella pneumoniae isolated from burn ulcers.
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Affiliation(s)
| | - Nafiseh Sadat Naghavi
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Monir Doudi
- Department of Microbiology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
| | - Ramesh Monajemi
- Department of Biology, Falavarjan Branch, Islamic Azad University, Isfahan, Iran
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24
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Jończyk-Matysiak E, Owczarek B, Popiela E, Świtała-Jeleń K, Migdał P, Cieślik M, Łodej N, Kula D, Neuberg J, Hodyra-Stefaniak K, Kaszowska M, Orwat F, Bagińska N, Mucha A, Belter A, Skupińska M, Bubak B, Fortuna W, Letkiewicz S, Chorbiński P, Weber-Dąbrowska B, Roman A, Górski A. Isolation and Characterization of Phages Active against Paenibacillus larvae Causing American Foulbrood in Honeybees in Poland. Viruses 2021; 13:1217. [PMID: 34201873 PMCID: PMC8310151 DOI: 10.3390/v13071217] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 06/17/2021] [Accepted: 06/21/2021] [Indexed: 12/15/2022] Open
Abstract
The aim of this study was the isolation and characterization, including the phage effect on honeybees in laboratory conditions, of phages active against Paenibacillus larvae, the causative agent of American Foulbrood-a highly infective and easily spreading disease occurring in honeybee larva, and subsequently the development of a preparation to prevent and treat this dangerous disease. From the tested material (over 2500 samples) 35 Paenibacillus spp. strains were obtained and used to search for phages. Five phages specific to Paenibacillus were isolated and characterized (ultrastructure, morphology, biological properties, storage stability, and genome sequence). The characteristics were performed to obtain knowledge of their lytic potential and compose the final phage cocktail with high antibacterial potential and intended use of future field application. Preliminary safety studies have also been carried out on healthy bees, which suggest that the phage preparation administered is harmless.
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Affiliation(s)
- Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland; (B.O.); (M.C.); (N.Ł.); (D.K.); (J.N.); (F.O.); (N.B.); (B.B.); (B.W.-D.); (A.G.)
| | - Barbara Owczarek
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland; (B.O.); (M.C.); (N.Ł.); (D.K.); (J.N.); (F.O.); (N.B.); (B.B.); (B.W.-D.); (A.G.)
| | - Ewa Popiela
- Department of Environment Hygiene and Animal Welfare, Wrocław University of Environmental and Life Sciences, Chełmońskiego Street 38C, 51-630 Wroclaw, Poland; (E.P.); (P.M.); (A.R.)
| | - Kinga Świtała-Jeleń
- Pure Biologics, Duńska Street 11, 54-427 Wroclaw, Poland; (K.Ś.-J.); (K.H.-S.)
| | - Paweł Migdał
- Department of Environment Hygiene and Animal Welfare, Wrocław University of Environmental and Life Sciences, Chełmońskiego Street 38C, 51-630 Wroclaw, Poland; (E.P.); (P.M.); (A.R.)
| | - Martyna Cieślik
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland; (B.O.); (M.C.); (N.Ł.); (D.K.); (J.N.); (F.O.); (N.B.); (B.B.); (B.W.-D.); (A.G.)
| | - Norbert Łodej
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland; (B.O.); (M.C.); (N.Ł.); (D.K.); (J.N.); (F.O.); (N.B.); (B.B.); (B.W.-D.); (A.G.)
| | - Dominika Kula
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland; (B.O.); (M.C.); (N.Ł.); (D.K.); (J.N.); (F.O.); (N.B.); (B.B.); (B.W.-D.); (A.G.)
| | - Joanna Neuberg
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland; (B.O.); (M.C.); (N.Ł.); (D.K.); (J.N.); (F.O.); (N.B.); (B.B.); (B.W.-D.); (A.G.)
| | | | - Marta Kaszowska
- Laboratory of Microbial Immunochemistry and Vaccines, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 54-427 Wrocław, Poland;
| | - Filip Orwat
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland; (B.O.); (M.C.); (N.Ł.); (D.K.); (J.N.); (F.O.); (N.B.); (B.B.); (B.W.-D.); (A.G.)
| | - Natalia Bagińska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland; (B.O.); (M.C.); (N.Ł.); (D.K.); (J.N.); (F.O.); (N.B.); (B.B.); (B.W.-D.); (A.G.)
| | - Anna Mucha
- Department of Genetics, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631 Wroclaw, Poland;
| | - Agnieszka Belter
- BioScientia, Ogrodowa Street 2/8, 61-820 Poznań, Poland; (A.B.); (M.S.)
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | | | - Barbara Bubak
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland; (B.O.); (M.C.); (N.Ł.); (D.K.); (J.N.); (F.O.); (N.B.); (B.B.); (B.W.-D.); (A.G.)
| | - Wojciech Fortuna
- Department of Neurosurgery, Wrocław Medical University, Borowska 213, 54-427 Wrocław, Poland;
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland;
| | - Sławomir Letkiewicz
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland;
- Department of Health Sciences, Jan Długosz University in Częstochowa, 12-200 Częstochowa, Poland
| | - Paweł Chorbiński
- Department of Epizootiology and Clinic of Birds and Exotic Animals, Wrocław University of Environmental and Life Sciences, pl. Grunwaldzki 45, 50-366 Wroclaw, Poland;
| | - Beata Weber-Dąbrowska
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland; (B.O.); (M.C.); (N.Ł.); (D.K.); (J.N.); (F.O.); (N.B.); (B.B.); (B.W.-D.); (A.G.)
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland;
| | - Adam Roman
- Department of Environment Hygiene and Animal Welfare, Wrocław University of Environmental and Life Sciences, Chełmońskiego Street 38C, 51-630 Wroclaw, Poland; (E.P.); (P.M.); (A.R.)
| | - Andrzej Górski
- Bacteriophage Laboratory, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland; (B.O.); (M.C.); (N.Ł.); (D.K.); (J.N.); (F.O.); (N.B.); (B.B.); (B.W.-D.); (A.G.)
- Phage Therapy Unit, Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Rudolf Weigl Street 12, 53-114 Wroclaw, Poland;
- Infant Jesus Hospital, The Medical University of Warsaw, 02-006 Warsaw, Poland
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Isolation and Characterization of a Novel Lytic Bacteriophage against the K2 Capsule-Expressing Hypervirulent Klebsiella pneumoniae Strain 52145, and Identification of Its Functional Depolymerase. Microorganisms 2021; 9:microorganisms9030650. [PMID: 33801047 PMCID: PMC8003838 DOI: 10.3390/microorganisms9030650] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/30/2022] Open
Abstract
Klebsiella pneumoniae is among the leading bacteria that cause nosocomial infections. The capsule of this Gram-negative bacterium is a dominant virulence factor, with a prominent role in defense and biofilm formation. Bacteriophages, which are specific for one bacterial strain and its capsule type, can evoke the lysis of bacterial cells, aided by polysaccharide depolymerase enzymes. In this study, we isolated and characterized a bacteriophage against the nosocomial K. pneumoniae 52145 strain with K2 capsular serotype. The phage showed a narrow host range and stable lytic activity, even when exposed to different temperatures or detergents. Preventive effect of the phage in a nasal colonization model was investigated in vivo. Phlyogenetic analysis showed that the newly isolated Klebsiella phage B1 belongs to the Webervirus genus in Drexlerviridae family. We identified the location of the capsule depolymerase gene of the new phage, which was amplified, cloned, expressed, and purified. The efficacy of the recombinant B1dep depolymerase was tested by spotting on K. pneumoniae strains and it was confirmed that the extract lowers the thickness of the bacterium lawn as it degrades the protective capsule on bacterial cells. As K. pneumoniae strains possessing the K2 serotype have epidemiological importance, the B1 phage and its depolymerase are promising candidates for use as possible antimicrobial agents.
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26
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Grabowski Ł, Łepek K, Stasiłojć M, Kosznik-Kwaśnicka K, Zdrojewska K, Maciąg-Dorszyńska M, Węgrzyn G, Węgrzyn A. Bacteriophage-encoded enzymes destroying bacterial cell membranes and walls, and their potential use as antimicrobial agents. Microbiol Res 2021; 248:126746. [PMID: 33773329 DOI: 10.1016/j.micres.2021.126746] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 01/22/2023]
Abstract
Appearance of pathogenic bacteria resistant to most, if not all, known antibiotics is currently one of the most significant medical problems. Therefore, development of novel antibacterial therapies is crucial for efficient treatment of bacterial infections in the near future. One possible option is to employ enzymes, encoded by bacteriophages, which cause destruction of bacterial cell membranes and walls. Bacteriophages use such enzymes to destroy bacterial host cells at the final stage of their lytic development, in order to ensure effective liberation of progeny virions. Nevertheless, to use such bacteriophage-encoded proteins in medicine and/or biotechnology, it is crucial to understand details of their biological functions and biochemical properties. Therefore, in this review article, we will present and discuss our current knowledge on the processes of bacteriophage-mediated bacterial cell lysis, with special emphasis on enzymes involved in them. Regulation of timing of the lysis is also discussed. Finally, possibilities of the practical use of these enzymes as antibacterial agents will be underlined and perspectives of this aspect will be presented.
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Affiliation(s)
- Łukasz Grabowski
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
| | - Krzysztof Łepek
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Małgorzata Stasiłojć
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Katarzyna Kosznik-Kwaśnicka
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
| | - Karolina Zdrojewska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Monika Maciąg-Dorszyńska
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
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27
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Ciepluch K, Skrzyniarz K, Zdańska J, Barrios-Gumiel A, Sánchez-Nieves J, de la Mata FJ, Maciejewska B, Drulis-Kawa Z, Bryszewska M, Arabski M. PEGylation of dendronized silver nanoparticles increases the binding affinity of antimicrobial proteins. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114339] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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28
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Bacteriophage-derived endolysins to target gram-negative bacteria. Int J Pharm 2020; 589:119833. [PMID: 32877733 DOI: 10.1016/j.ijpharm.2020.119833] [Citation(s) in RCA: 62] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 08/18/2020] [Accepted: 08/26/2020] [Indexed: 12/24/2022]
Abstract
Bacteriophage-encoded endolysins (lysins) have emerged as a novel class of antibacterial agents to combat the surging antibiotic resistance. Lysins have specific structures and mechanisms to exert antibacterial effect against both Gram-positive (G+ve) and Gram-negative (G-ve) bacteria. However, its use against G-ve bacteria is limited because the outer membrane (OM) of G-ve bacteria hinders the permeation of exogenously applied lysins. Besides identifying lysins with intrinsic OM permeability, several other approaches including combining lysins with outer membrane permeabilizers (OMPs), protein engineering and formulating with nanocarriers have been proposed to enhance the permeability and activity of lysins. In the present review, we summarize strategies that have been developed to enable lysins to target G-ve bacteria in the past decade. While lysins demonstrates clear potential in managing bacterial infections caused by the drug-resistant G-ve bacteria, there are still challenges hindering their translation into clinical settings, including safety issues with OMP use, low efficiency against stationary phase bacteria and problems in stability. The applicability of protein engineering and formulation sciences to improve enzyme stability, and combination therapy with other classes of antibacterial agents to maximize the therapeutic potential have also been reviewed.
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29
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Bleriot I, Trastoy R, Blasco L, Fernández-Cuenca F, Ambroa A, Fernández-García L, Pacios O, Perez-Nadales E, Torre-Cisneros J, Oteo-Iglesias J, Navarro F, Miró E, Pascual A, Bou G, Martínez-Martínez L, Tomas M. Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae. Microb Genom 2020; 6:e000369. [PMID: 32375972 PMCID: PMC7371120 DOI: 10.1099/mgen.0.000369] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/31/2020] [Indexed: 12/12/2022] Open
Abstract
Klebsiella pneumoniae is the clinically most important species within the genus Klebsiella and, as a result of the continuous emergence of multi-drug resistant (MDR) strains, the cause of severe nosocomial infections. The decline in the effectiveness of antibiotic treatments for infections caused by MDR bacteria has generated particular interest in the study of bacteriophages. In this study, we characterized a total of 40 temperate bacteriophages (prophages) with a genome range of 11.454-84.199 kb, predicted from 16 carbapenemase-producing clinical strains of K. pneumoniae belonging to different sequence types, previously identified by multilocus sequence typing. These prophages were grouped into the three families in the order Caudovirales (27 prophages belonging to the family Myoviridae, 10 prophages belonging to the family Siphoviridae and 3 prophages belonging to the family Podoviridae). Genomic comparison of the 40 prophage genomes led to the identification of four prophages isolated from different strains and of genome sizes of around 33.3, 36.1, 39.6 and 42.6 kb. These prophages showed sequence similarities (query cover >90 %, identity >99.9 %) with international Microbe Versus Phage (MVP) (http://mvp.medgenius.info/home) clusters 4762, 4901, 3499 and 4280, respectively. Phylogenetic analysis revealed the evolutionary proximity among the members of the four groups of the most frequently identified prophages in the bacterial genomes studied (33.3, 36.1, 39.6 and 42.6 kb), with bootstrap values of 100 %. This allowed the prophages to be classified into three clusters: A, B and C. Interestingly, these temperate bacteriophages did not infect the highest number of strains as indicated by a host-range assay, these results could be explained by the development of superinfection exclusion mechanisms. In addition, bioinformatic analysis of the 40 identified prophages revealed the presence of 2363 proteins. In total, 59.7 % of the proteins identified had a predicted function, mainly involving viral structure, transcription, replication and regulation (lysogenic/lysis). Interestingly, some proteins had putative functions associated with bacterial virulence (toxin expression and efflux pump regulators), phage defence profiles such as toxin-antitoxin modules, an anti-CRISPR/Cas9 protein, TerB protein (from terZABCDE operon) and methyltransferase proteins.
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Affiliation(s)
- Ines Bleriot
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Rocío Trastoy
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Lucia Blasco
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Felipe Fernández-Cuenca
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena. Deparment of Microbiology and Medicine, University of Seville, Seville, Spain
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
| | - Antón Ambroa
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Laura Fernández-García
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Olga Pacios
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Elena Perez-Nadales
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Microbiology Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Cordoba, Spain
| | - Julian Torre-Cisneros
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Microbiology Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Cordoba, Spain
| | - Jesús Oteo-Iglesias
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Ferran Navarro
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Microbiology Department, Sant Pau Hospital, Autonomous University of Barcelona (Bellaterra), Barcelona, Spain
| | - Elisenda Miró
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Microbiology Department, Sant Pau Hospital, Autonomous University of Barcelona (Bellaterra), Barcelona, Spain
| | - Alvaro Pascual
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena. Deparment of Microbiology and Medicine, University of Seville, Seville, Spain
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
| | - German Bou
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
| | - Luis Martínez-Martínez
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Microbiology Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Cordoba, Spain
| | - Maria Tomas
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
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Gram-Negative Bacterial Lysins. Antibiotics (Basel) 2020; 9:antibiotics9020074. [PMID: 32054067 PMCID: PMC7168136 DOI: 10.3390/antibiotics9020074] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 02/06/2020] [Accepted: 02/07/2020] [Indexed: 12/13/2022] Open
Abstract
Antibiotics have had a profound impact on human society by enabling the eradication of otherwise deadly infections. Unfortunately, antibiotic use and overuse has led to the rapid spread of acquired antibiotic resistance, creating a major threat to public health. Novel therapeutic agents called bacteriophage endolysins (lysins) provide a solution to the worldwide epidemic of antibiotic resistance. Lysins are a class of enzymes produced by bacteriophages during the lytic cycle, which are capable of cleaving bonds in the bacterial cell wall, resulting in the death of the bacteria within seconds after contact. Through evolutionary selection of the phage progeny to be released and spread, these lysins target different critical components in the cell wall, making resistance to these molecules orders of magnitude less likely than conventional antibiotics. Such properties make lysins uniquely suitable for the treatment of multidrug resistant bacterial pathogens. Lysins, either naturally occurring or engineered, have the potential of being developed into fast-acting, narrow-spectrum, biofilm-disrupting antimicrobials that act synergistically with standard of care antibiotics. This review focuses on newly discovered classes of Gram-negative lysins with emphasis on prototypical enzymes that have been evaluated for efficacy against the major antibiotic resistant organisms causing nosocomial infections.
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31
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Herridge WP, Shibu P, O’Shea J, Brook TC, Hoyles L. Bacteriophages of Klebsiella spp., their diversity and potential therapeutic uses. J Med Microbiol 2020; 69:176-194. [PMID: 31976857 PMCID: PMC7431098 DOI: 10.1099/jmm.0.001141] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/20/2019] [Indexed: 12/16/2022] Open
Abstract
Klebsiella spp. are commensals of the human microbiota, and a leading cause of opportunistic nosocomial infections. The incidence of multidrug resistant (MDR) strains of Klebsiella pneumoniae causing serious infections is increasing, and Klebsiella oxytoca is an emerging pathogen. Alternative strategies to tackle infections caused by these bacteria are required as strains become resistant to last-resort antibiotics such as colistin. Bacteriophages (phages) are viruses that can infect and kill bacteria. They and their gene products are now being considered as alternatives or adjuncts to antimicrobial therapies. Several in vitro and in vivo studies have shown the potential for lytic phages to combat MDR K. pneumoniae infections. Ready access to cheap sequencing technologies has led to a large increase in the number of genomes available for Klebsiella-infecting phages, with these phages being heterogeneous at the whole-genome level. This review summarizes our current knowledge on phages of Klebsiella spp. and highlights technological and biological issues relevant to the development of phage-based therapies targeting these bacteria.
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Affiliation(s)
- Warren P. Herridge
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Preetha Shibu
- Life Sciences, University of Westminster, 115 Cavendish Street, London W1W 6UW, UK
| | - Jessica O’Shea
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Thomas C. Brook
- Life Sciences, University of Westminster, 115 Cavendish Street, London W1W 6UW, UK
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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32
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Ciepluch K, Skrzyniarz K, Barrios-Gumiel A, Quintana S, Sánchez-Nieves J, de la Mata FJ, Maciejewska B, Drulis-Kawa Z, Arabski M. Dendronized Silver Nanoparticles as Bacterial Membrane Permeabilizers and Their Interactions With P. aeruginosa Lipopolysaccharides, Lysozymes, and Phage-Derived Endolysins. Front Microbiol 2019; 10:2771. [PMID: 31866964 PMCID: PMC6908850 DOI: 10.3389/fmicb.2019.02771] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/13/2019] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial proteins, like lysozymes produced by animals or bacteriophage lysins, enable the degradation of bacterial peptidoglycan (PG) and, consequently, lead to bacterial cell lysis. However, the activity of those enzymes is not satisfactory against gram-negative bacteria because of the presence of an outer membrane (OM) barrier. Lytic enzymes can therefore be combined with membrane-disrupting agents, such as dendritic silver nanoparticles. Nevertheless, a lipopolysaccharide (LPS), especially the smooth type, could be the main hindrance for highly charged nanoparticles to get direct access to the bacterial OM and to help lytic enzymes to reach their target PG. Herein, we have investigated the interactions of PEGylated carbosilane dendritic nanoparticles with P. aeruginosa 010 LPS in the presence of lysozymes and KP27 endolysin to find out the main aspects of the OM destabilization process. Our results showed that PEGylated dendronized AgNPs overcame the LPS barrier and enhanced the antibacterial effect of endolysin more efficiently than unPEGylated nanoparticles.
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Affiliation(s)
- Karol Ciepluch
- Department of Biochemistry and Genetics, Jan Kochanowski University, Kielce, Poland
| | - Kinga Skrzyniarz
- Department of Biochemistry and Genetics, Jan Kochanowski University, Kielce, Poland
| | - Andrea Barrios-Gumiel
- Department of Organic and Inorganic Chemistry, Chemistry Research Institute "Andrés M. del Río" (IQAR), University of Alcalá, Madrid, Spain.,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain.,Institute Ramón y Cajal for Health Research (IRYCIS), Madrid, Spain
| | - Sara Quintana
- Department of Organic and Inorganic Chemistry, Chemistry Research Institute "Andrés M. del Río" (IQAR), University of Alcalá, Madrid, Spain.,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Javier Sánchez-Nieves
- Department of Organic and Inorganic Chemistry, Chemistry Research Institute "Andrés M. del Río" (IQAR), University of Alcalá, Madrid, Spain.,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain.,Institute Ramón y Cajal for Health Research (IRYCIS), Madrid, Spain
| | - F Javier de la Mata
- Department of Organic and Inorganic Chemistry, Chemistry Research Institute "Andrés M. del Río" (IQAR), University of Alcalá, Madrid, Spain.,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Madrid, Spain.,Institute Ramón y Cajal for Health Research (IRYCIS), Madrid, Spain
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wrocław, Wrocław, Poland
| | - Michał Arabski
- Department of Biochemistry and Genetics, Jan Kochanowski University, Kielce, Poland
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33
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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: 101] [Impact Index Per Article: 16.8] [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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34
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Amiri Fahliyani S, Beheshti-Maal K, Ghandehari F. Novel lytic bacteriophages of Klebsiella oxytoca ABG-IAUF-1 as the potential agents for mastitis phage therapy. FEMS Microbiol Lett 2019; 365:5096019. [PMID: 30212876 DOI: 10.1093/femsle/fny223] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Accepted: 09/09/2018] [Indexed: 01/05/2023] Open
Abstract
Mastitis is an inflammation of the mammary gland that occurs when pathogenic microorganisms enter the udder. Even though tremendous advancements in veterinary diagnosis and therapeutics, mastitis is still the most frequent and costly disease of dairy herds overall the world. The purpose of this research was to isolate and identify the lytic phages as a potential method for biological control of bovine mastitis. In this study Klebsiella oxytoca was isolated from contaminated milk samples of Isfahan dairy herds, Isfahan, Iran and characterized as K. oxytoca ABG-IAUF-1 and its 16s-rRNA sequence was deposited in GenBank under the accession numbers of MF175803.1. Then, the four novel specific lytic bacteriophages of K. oxytoca ABG-IAUF-1 from Isfahan public wastewater were isolated and identified. The results of transmission electron microscopy indicated that theses isolated phages were related to Myoviridae and Podoviridae families of bacteriophages. Also the analysis of the growth curve of K. oxytoca ABG-IAUF-1 before and after treatment with lytic phage showed the 97% success rate of the phages in preventing of bacterial growth. This is the first report indicating the use of bacteriophages as the potential agents for eliminating the pathogenic bacteria responsible for bovine mastitis in Iran. The applications of these lytic phages could be an asset for biocontrolling of pathogenic agents in medical and veterinary biotechnology.
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Affiliation(s)
- Sara Amiri Fahliyani
- Department of Microbiology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Falavarjan 84515/155, Isfahan, Iran
| | - Keivan Beheshti-Maal
- Department of Microbiology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Falavarjan 84515/155, Isfahan, Iran
| | - Fereshteh Ghandehari
- Department of Microbiology, Faculty of Biological Sciences, Falavarjan Branch, Islamic Azad University, Falavarjan 84515/155, Isfahan, Iran
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35
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Ciepluch K, Maciejewska B, Gałczyńska K, Kuc-Ciepluch D, Bryszewska M, Appelhans D, Drulis-Kawa Z, Arabski M. The influence of cationic dendrimers on antibacterial activity of phage endolysin against P. aeruginosa cells. Bioorg Chem 2019; 91:103121. [DOI: 10.1016/j.bioorg.2019.103121] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 06/28/2019] [Accepted: 07/11/2019] [Indexed: 01/21/2023]
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36
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Gałczyńska K, Ciepluch K, Madej Ł, Kurdziel K, Maciejewska B, Drulis-Kawa Z, Węgierek-Ciuk A, Lankoff A, Arabski M. Selective cytotoxicity and antifungal properties of copper(II) and cobalt(II) complexes with imidazole-4-acetate anion or 1-allylimidazole. Sci Rep 2019; 9:9777. [PMID: 31278366 PMCID: PMC6611867 DOI: 10.1038/s41598-019-46224-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Accepted: 06/19/2019] [Indexed: 12/23/2022] Open
Abstract
The physicochemical properties of metal complexes determine their potential applications as antitumor agents. In this study, the antitumor properties of mononuclear cobalt(II) and copper(II) coordination compounds (stoichiometry: [Co(iaa)2(H2O)2]·H2O (iaa = imidazole-4-acetate anion), [Co(1-allim)6](NO3)2 (1-allim = 1-allylimidazole), [Cu(iaa)2H2O] and [Cu(1-allim)4(NO3)2]) and their ligands have been evaluated on human lung carcinoma A549 cells and normal bronchial BEAS-2B cells. Designing the chemical structure of new antitumor agents the possible interactions with macromolecules such as DNA or proteins should be take into account. PCR gene tlr4 product served as DNA model, whereas lysozyme and phage-derived endolysin (both peptidoglycan degrading enzymes) were applied as protein/enzyme model. The interactions were analysed using PCR-HRM and circular dichroism, FT-IR, spectrophotometry, respectively. Additionally, the antimicrobial properties of the complexes at a non-cytotoxic concentration were analyzed against S. aureus, E. coli, P. aeruginosa and C. albicans strains. The results obtained in this study showed the selective cytotoxicity of metal complexes, mainly [Cu(1-allim)4(NO3)2] towards tumor cells. From all tested compounds, only [Co(iaa)2(H2O)2].H2O non-covalently interacts with DNA. Cu(II) and Co(II) complexes did not affect the secondary conformation of tested proteins but modified the hydrolytic activity of enzymes (lysozyme and endolysin). Moreover, only [Co(iaa)2(H2O)2].H2O exhibited the antifungal properties. In conclusion, Co(II) and Cu(II) metal complexes bearing two imidazole-4-acetate ligands seemed to be promising antitumor and antifungal agents for future drug design and application.
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Affiliation(s)
- Katarzyna Gałczyńska
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, Świętokrzyska 15, 25-406, Kielce, Poland
| | - Karol Ciepluch
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, Świętokrzyska 15, 25-406, Kielce, Poland
| | - Łukasz Madej
- Holy Cross Oncology Center of Kielce, Artwińskiego 3, 25-734, Kielce, Poland
| | - Krystyna Kurdziel
- Institute of Chemistry, Jan Kochanowski University, Świętokrzyska 15G, 25-406, Kielce, Poland
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63-77, 51-148, Wrocław, Poland
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63-77, 51-148, Wrocław, Poland
| | - Aneta Węgierek-Ciuk
- Department of Radiobiology and Immunology, Jan Kochanowski University, Świętokrzyska 15, 25-406, Kielce, Poland
| | - Anna Lankoff
- Department of Radiobiology and Immunology, Jan Kochanowski University, Świętokrzyska 15, 25-406, Kielce, Poland.,Center for Radiobiology and Biological Dosimetry, Institute of Nuclear Chemistry and Technology, Dorodna 16, 03-195, Warsaw, Poland
| | - Michał Arabski
- Department of Biochemistry and Genetics, Institute of Biology, Jan Kochanowski University, Świętokrzyska 15, 25-406, Kielce, Poland.
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37
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Zhao J, Zhang Z, Tian C, Chen X, Hu L, Wei X, Li H, Lin W, Jiang A, Feng R, Yuan J, Yin Z, Zhao X. Characterizing the Biology of Lytic Bacteriophage vB_EaeM_φEap-3 Infecting Multidrug-Resistant Enterobacter aerogenes. Front Microbiol 2019; 10:420. [PMID: 30891025 PMCID: PMC6412083 DOI: 10.3389/fmicb.2019.00420] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/18/2019] [Indexed: 12/24/2022] Open
Abstract
Carbapenem-resistant Enterobacter aerogenes strains are a major clinical problem because of the lack of effective alternative antibiotics. However, viruses that lyze bacteria, called bacteriophages, have potential therapeutic applications in the control of antibiotic-resistant bacteria. In the present study, a lytic bacteriophage specific for E. aerogenes isolates, designated vB_EaeM_φEap-3, was characterized. Based on transmission electron microscopy analysis, phage vB_EaeM_φEap-3 was classified as a member of the family Myoviridae (order, Caudovirales). Host range determination revealed that vB_EaeM_φEap-3 lyzed 18 of the 28 E. aerogenes strains tested, while a one-step growth curve showed a short latent period and a moderate burst size. The stability of vB_EaeM_φEap-3 at various temperatures and pH levels was also examined. Genomic sequencing and bioinformatics analysis revealed that vB_EaeM_φEap-3 has a 175,814-bp double-stranded DNA genome that does not contain any genes considered undesirable for the development of therapeutics (e.g., antibiotic resistance genes, toxin-encoding genes, integrase). The phage genome contained 278 putative protein-coding genes and one tRNA gene, tRNA-Met (AUG). Phylogenetic analysis based on large terminase subunit and major capsid protein sequences suggested that vB_EaeM_φEap-3 belongs to novel genus “Kp15 virus” within the T4-like virus subfamily. Based on host range, genomic, and physiological parameters, we propose that phage vB_EaeM_φEap-3 is a suitable candidate for phage therapy applications.
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Affiliation(s)
- Jiangtao Zhao
- Department of Histology and Embryology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zheng Zhang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Changyu Tian
- Institute of Disease Control and Prevention, Chinese People's Liberation Army (PLA), Beijing, China
| | - Xiao Chen
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Lingfei Hu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiao Wei
- Institute of Disease Control and Prevention, Chinese People's Liberation Army (PLA), Beijing, China
| | - Huan Li
- Institute of Disease Control and Prevention, Chinese People's Liberation Army (PLA), Beijing, China
| | - Weishi Lin
- Institute of Disease Control and Prevention, Chinese People's Liberation Army (PLA), Beijing, China
| | - Aimin Jiang
- College of Food Science, South China Agricultural University, Guangzhou, China
| | - Ruo Feng
- Department of Histology and Embryology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China
| | - Jing Yuan
- Institute of Disease Control and Prevention, Chinese People's Liberation Army (PLA), Beijing, China
| | - Zhe Yin
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Xiangna Zhao
- Institute of Disease Control and Prevention, Chinese People's Liberation Army (PLA), Beijing, China
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38
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Vázquez R, García E, García P. Phage Lysins for Fighting Bacterial Respiratory Infections: A New Generation of Antimicrobials. Front Immunol 2018; 9:2252. [PMID: 30459750 PMCID: PMC6232686 DOI: 10.3389/fimmu.2018.02252] [Citation(s) in RCA: 81] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 09/11/2018] [Indexed: 01/03/2023] Open
Abstract
Lower respiratory tract infections and tuberculosis are responsible for the death of about 4.5 million people each year and are the main causes of mortality in children under 5 years of age. Streptococcus pneumoniae is the most common bacterial pathogen associated with severe pneumonia, although other Gram-positive and Gram-negative bacteria are involved in respiratory infections as well. The ability of these pathogens to persist and produce infection under the appropriate conditions is also associated with their capacity to form biofilms in the respiratory mucous membranes. Adding to the difficulty of treating biofilm-forming bacteria with antibiotics, many of these strains are becoming multidrug resistant, and thus the alternative therapeutics available for combating this kind of infections are rapidly depleting. Given these concerns, it is urgent to consider other unconventional strategies and, in this regard, phage lysins represent an attractive resource to circumvent some of the current issues in infection treatment. When added exogenously, lysins break specific bonds of the peptidoglycan and have potent bactericidal effects against susceptible bacteria. These enzymes possess interesting features, including that they do not trigger an adverse immune response and raise of resistance is very unlikely. Although Gram-negative bacteria had been considered refractory to these compounds, strategies to overcome this drawback have been developed recently. In this review we describe the most relevant in vitro and in vivo results obtained to date with lysins against bacterial respiratory pathogens.
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Affiliation(s)
- Roberto Vázquez
- Centro de Investigaciones Biológicas (CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Ernesto García
- Centro de Investigaciones Biológicas (CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
| | - Pedro García
- Centro de Investigaciones Biológicas (CSIC), Madrid, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES), Madrid, Spain
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39
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Mikoulinskaia GV, Chernyshov SV, Shavrina MS, Molochkov NV, Lysanskaya VY, Zimin AA. Two novel thermally resistant endolysins encoded by pseudo T-even bacteriophages RB43 and RB49. J Gen Virol 2018; 99:402-415. [DOI: 10.1099/jgv.0.001014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- Galina V. Mikoulinskaia
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry RAS, Pushchino, Moscow region 142290, Russia
| | - Sergei V. Chernyshov
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry RAS, Pushchino, Moscow region 142290, Russia
| | - Maria S. Shavrina
- Branch of Shemyakin & Ovchinnikov’s Institute of Bioorganic Chemistry RAS, Pushchino, Moscow region 142290, Russia
| | - Nikolai V. Molochkov
- Institute of Theoretical and Experimental Biophysics RAS, Pushchino, Moscow region 142290, Russia
| | - Valentina Ya. Lysanskaya
- Skryabin’s Institute of Biochemistry and Physiology of Micro-organisms RAS, Pushchino, Moscow region 142290, Russia
| | - Andrei A. Zimin
- Skryabin’s Institute of Biochemistry and Physiology of Micro-organisms RAS, Pushchino, Moscow region 142290, Russia
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40
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Maciejewska B, Olszak T, Drulis-Kawa Z. Applications of bacteriophages versus phage enzymes to combat and cure bacterial infections: an ambitious and also a realistic application? Appl Microbiol Biotechnol 2018; 102:2563-2581. [PMID: 29442169 PMCID: PMC5847195 DOI: 10.1007/s00253-018-8811-1] [Citation(s) in RCA: 124] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 01/22/2018] [Accepted: 01/23/2018] [Indexed: 01/21/2023]
Abstract
Bacteriophages (phages) are viruses that infect bacteria. The "predator-prey" interactions are recognized as a potentially effective way to treat infections. Phages, as well as phage-derived proteins, especially enzymes, are intensively studied to become future alternative or supportive antibacterials used alone or in combination with standard antibiotic regimens treatment. There are many publications presenting phage therapy aspects, and some papers focused separately on the application of phage-derived enzymes. In this review, we discuss advantages and limitations of both agents concerning their specificity, mode of action, structural issues, resistance development, pharmacokinetics, product preparation, and interactions with the immune system. Finally, we describe the current regulations for phage-based product application.
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Affiliation(s)
- Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, S. Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Tomasz Olszak
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, S. Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, S. Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.
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41
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BluePharmTrain: Biology and Biotechnology of Marine Sponges. GRAND CHALLENGES IN MARINE BIOTECHNOLOGY 2018. [DOI: 10.1007/978-3-319-69075-9_13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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42
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Brzozowska E, Pyra A, Pawlik K, Janik M, Górska S, Urbańska N, Drulis-Kawa Z, Gamian A. Hydrolytic activity determination of Tail Tubular Protein A of Klebsiella pneumoniae bacteriophages towards saccharide substrates. Sci Rep 2017; 7:18048. [PMID: 29273737 PMCID: PMC5741709 DOI: 10.1038/s41598-017-18096-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 12/06/2017] [Indexed: 01/26/2023] Open
Abstract
In this paper, the enzymatic activity, substrate specificity and antibiofilm feature of bacteriophage dual-function tail proteins are presented. So far, tail tubular proteins A–TTPAgp31 and TTPAgp44-have been considered as structural proteins of Klebsiella pneumoniae bacteriophages KP32 and KP34, respectively. Our results show that TTPAgp31 is able to hydrolyze maltose as well as Red-starch. The activity of 1 µM of the protein was calculated as 47.6 milli-Units/assay relating to the α-amylase activity. It degrades capsular polysaccharides (cPS), slime polysaccharides (sPS) and lipopolysaccharide (LPS) of K. pneumoniae PCM 2713 and shows antibiofilm reactivity towards S. aureus PCM 519 and E. faecalis PCM 2673. TTPAgp44 hydrolyses trehalose and cPS of E. faecium PCM 1859. TTPAgp44′s activity was also observed in the antibiofilm test against P. aeruginosa PCM 2710 and B. subtilis PCM 2021. TTPAgp31 has been identified as α-1,4-glucosidase whereas, TTPAgp44 exhibits trehalase-like activity. Both proteins contain aspartate and glutamate residues in the β-stranded region which are essential for catalytic activity of glycoside hydrolases. The significant novelty of our results is that for the first time the bacteriophage tubular proteins are described as the unique enzymes displaying no similarity to any known phage hydrolases. They can be used as antibacterial agents directed against bacterial strains producing exopolysaccharides and forming a biofilm.
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Affiliation(s)
- Ewa Brzozowska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 R. Weigl, 53-114, Wroclaw, Poland.
| | - Anna Pyra
- Faculty of Chemistry, Department of Crystallography, University of Wroclaw, 14 F. Joliot-Curie, 50-383, Wroclaw, Poland.
| | - Krzysztof Pawlik
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 R. Weigl, 53-114, Wroclaw, Poland
| | - Monika Janik
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 R. Weigl, 53-114, Wroclaw, Poland
| | - Sabina Górska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 R. Weigl, 53-114, Wroclaw, Poland
| | - Natalia Urbańska
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 R. Weigl, 53-114, Wroclaw, Poland.,Department of Biological Science, University of Wroclaw, 35 Kuznicza, 50-138, Wroclaw, Poland
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 63-77 Przybyszewskiego, 51-148, Wroclaw, Poland
| | - Andrzej Gamian
- Ludwik Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 R. Weigl, 53-114, Wroclaw, Poland.,Wroclaw Research Center EIT+, 147 Stablowicka, 54-066, Wroclaw, Poland
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43
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Maciejewska B, Źrubek K, Espaillat A, Wiśniewska M, Rembacz KP, Cava F, Dubin G, Drulis-Kawa Z. Modular endolysin of Burkholderia AP3 phage has the largest lysozyme-like catalytic subunit discovered to date and no catalytic aspartate residue. Sci Rep 2017; 7:14501. [PMID: 29109551 PMCID: PMC5674055 DOI: 10.1038/s41598-017-14797-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/16/2017] [Indexed: 01/19/2023] Open
Abstract
Endolysins are peptidoglycan-degrading enzymes utilized by bacteriophages to release the progeny from bacterial cells. The lytic properties of phage endolysins make them potential antibacterial agents for medical and industrial applications. Here, we present a comprehensive characterization of phage AP3 modular endolysin (AP3gp15) containing cell wall binding domain and an enzymatic domain (DUF3380 by BLASTP), both widespread and conservative. Our structural analysis demonstrates the low similarity of an enzymatic domain to known lysozymes and an unusual catalytic centre characterized by only a single glutamic acid residue and no aspartic acid. Thus, our findings suggest distinguishing a novel class of muralytic enzymes having the activity and catalytic centre organization of DUF3380. The lack of amino acid sequence homology between AP3gp15 and other known muralytic enzymes may reflect the evolutionary convergence of analogous glycosidases. Moreover, the broad antibacterial spectrum, lack of cytotoxic effect on human cells and the stability characteristics of AP3 endolysin advocate for its future application development.
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Affiliation(s)
- Barbara Maciejewska
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Karol Źrubek
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Akbar Espaillat
- Laboratory for Molecular Infection Medicine Sweden. Molecular Biology Department, Umeå University, SE-901 87, Umeå, Sweden
| | - Magdalena Wiśniewska
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Krzysztof P Rembacz
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Krakow, Poland
| | - Felipe Cava
- Laboratory for Molecular Infection Medicine Sweden. Molecular Biology Department, Umeå University, SE-901 87, Umeå, Sweden
| | - Grzegorz Dubin
- Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387, Kraków, Poland.
- Protein Crystallography Research Group, Malopolska Centre of Biotechnology, Gronostajowa 7A, 30-387, Krakow, Poland.
| | - Zuzanna Drulis-Kawa
- Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.
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Latka A, Maciejewska B, Majkowska-Skrobek G, Briers Y, Drulis-Kawa Z. Bacteriophage-encoded virion-associated enzymes to overcome the carbohydrate barriers during the infection process. Appl Microbiol Biotechnol 2017; 101:3103-3119. [PMID: 28337580 PMCID: PMC5380687 DOI: 10.1007/s00253-017-8224-6] [Citation(s) in RCA: 242] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 02/23/2017] [Accepted: 03/04/2017] [Indexed: 11/24/2022]
Abstract
Bacteriophages are bacterial viruses that infect the host after successful receptor recognition and adsorption to the cell surface. The irreversible adherence followed by genome material ejection into host cell cytoplasm must be preceded by the passage of diverse carbohydrate barriers such as capsule polysaccharides (CPSs), O-polysaccharide chains of lipopolysaccharide (LPS) molecules, extracellular polysaccharides (EPSs) forming biofilm matrix, and peptidoglycan (PG) layers. For that purpose, bacteriophages are equipped with various virion-associated carbohydrate active enzymes, termed polysaccharide depolymerases and lysins, that recognize, bind, and degrade the polysaccharide compounds. We discuss the existing diversity in structural locations, variable architectures, enzymatic specificities, and evolutionary aspects of polysaccharide depolymerases and virion-associated lysins (VALs) and illustrate how these aspects can correlate with the host spectrum. In addition, we present methods that can be used for activity determination and the application potential of these enzymes as antibacterials, antivirulence agents, and diagnostic tools.
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Affiliation(s)
- Agnieszka Latka
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.,Laboratory of Applied Biotechnology, Department of Applied Biosciences, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Grazyna Majkowska-Skrobek
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Applied Biosciences, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.
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