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Chong Qui E, Habtehyimer F, Germroth A, Grant J, Kosanovic L, Singh I, Hancock SP. Mycobacteriophage Alexphander Gene 94 Encodes an Essential dsDNA-Binding Protein during Lytic Infection. Int J Mol Sci 2024; 25:7466. [PMID: 39000573 PMCID: PMC11242194 DOI: 10.3390/ijms25137466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Revised: 06/28/2024] [Accepted: 07/01/2024] [Indexed: 07/16/2024] Open
Abstract
Mycobacteriophages are viruses that specifically infect bacterial species within the genera Mycobacterium and Mycolicibacterium. Over 2400 mycobacteriophages have been isolated on the host Mycolicibacterium smegmatis and sequenced. This wealth of genomic data indicates that mycobacteriophage genomes are diverse, mosaic, and contain numerous (35-60%) genes for which there is no predicted function based on sequence similarity to characterized orthologs, many of which are essential to lytic growth. To fully understand the molecular aspects of mycobacteriophage-host interactions, it is paramount to investigate the function of these genes and gene products. Here we show that the temperate mycobacteriophage, Alexphander, makes stable lysogens with a frequency of 2.8%. Alexphander gene 94 is essential for lytic infection and encodes a protein predicted to contain a C-terminal MerR family helix-turn-helix DNA-binding motif (HTH) and an N-terminal DinB/YfiT motif, a putative metal-binding motif found in stress-inducible gene products. Full-length and C-terminal gp94 constructs form high-order nucleoprotein complexes on 100-500 base pair double-stranded DNA fragments and full-length phage genomic DNA with little sequence discrimination for the DNA fragments tested. Maximum gene 94 mRNA levels are observed late in the lytic growth cycle, and gene 94 is transcribed in a message with neighboring genes 92 through 96. We hypothesize that gp94 is an essential DNA-binding protein for Alexphander during lytic growth. We proposed that gp94 forms multiprotein complexes on DNA through cooperative interactions involving its HTH DNA-binding motif at sites throughout the phage chromosome, facilitating essential DNA transactions required for lytic propagation.
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Affiliation(s)
| | | | | | | | | | | | - Stephen P. Hancock
- Department of Chemistry, Towson University, Towson, MD 21252, USA; (E.C.Q.); (F.H.); (A.G.); (J.G.); (L.K.); (I.S.)
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2
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Li S, Xu M, Yang D, Yang M, Wu H, Li X, Yang C, Fang Z, Wu Q, Tan L, Xiao W, Weng Q. Characterization and genomic analysis of a lytic Stenotrophomonas maltophilia short-tailed phage A1432 revealed a new genus of the family Mesyanzhinovviridae. Front Microbiol 2024; 15:1400700. [PMID: 38993489 PMCID: PMC11236537 DOI: 10.3389/fmicb.2024.1400700] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 06/14/2024] [Indexed: 07/13/2024] Open
Abstract
Stenotrophomonas maltophilia (S. maltophilia) is an emerging opportunistic pathogen that exhibits resistant to a majority of commonly used antibiotics. Phages have the potential to serve as an alternative treatment for S. maltophilia infections. In this study, a lytic phage, A1432, infecting S. maltophilia YCR3A-1, was isolated and characterized from a karst cave. Transmission electron microscopy revealed that phage A1432 possesses an icosahedral head and a shorter tail. Phage A1432 demonstrated a narrow host range, with an optimal multiplicity of infection of 0.1. The one-step growth curve indicated a latent time of 10 min, a lysis period of 90 min, a burst size of 43.2 plaque-forming units per cell. In vitro bacteriolytic activity test showed that phage A1432 was capable to inhibit the growth of S. maltophilia YCR3A-1 in an MOI-dependent manner after 2 h of co-culture. BLASTn analysis showed that phage A1432 genome shares the highest similarity (81.46%) with Xanthomonas phage Xoo-sp2 in the NCBI database, while the query coverage was only 37%. The phage contains double-stranded DNA with a genome length of 61,660 bp and a GC content of 61.92%. It is predicted to have 79 open reading frames and one tRNA, with no virulence or antibiotic resistance genes. Phylogenetic analysis using terminase large subunit and DNA polymerase indicated that phage A1432 clustered with members of the Bradleyvirinae subfamily but diverged into a distinct branch. Further phylogenetic comparison analysis using Average Nucleotide Identity, proteomic phylogenetic analysis, genomic network analysis confirmed that phage A1432 belongs to a novel genus within the Bradleyvirinae subfamily, Mesyanzhinovviridae family. Additionally, phylogenetic analysis of the so far isolated S. maltophilia phages revealed significant genetic diversity among these phages. The results of this research will contribute valuable information for further studies on their morphological and genetic diversity, will aid in elucidating the evolutionary mechanisms that give rise to them.
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Affiliation(s)
- Shixia Li
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Man Xu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Deying Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Mei Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Hejing Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Xuelian Li
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Changzhou Yang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Zheng Fang
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Qingshan Wu
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Leitao Tan
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Wei Xiao
- Yunnan Institute of Microbiology, Yunnan International Joint Laboratory of Virology and Immunology, Yunnan University, Kunming, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang, China
- Qiannan Normal University for Nationalities, Duyun, China
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Li L, Zhang H, Jin H, Guo J, Liu P, Yang J, Wang Z, Zhang E, Yu B, Shi L, He J, Wang P, Wei J, Zhong Y, Li W. Identification and characterization of two Bacillus anthracis bacteriophages. Arch Virol 2024; 169:134. [PMID: 38834736 PMCID: PMC11150296 DOI: 10.1007/s00705-024-06005-7] [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: 10/08/2023] [Accepted: 02/05/2024] [Indexed: 06/06/2024]
Abstract
Anthrax is an acute infectious zoonotic disease caused by Bacillus anthracis, a bacterium that is considered a potential biological warfare agent. Bacillus bacteriophages shape the composition and evolution of bacterial communities in nature and therefore have important roles in the ecosystem community. B. anthracis phages are not only used in etiological diagnostics but also have promising prospects in clinical therapeutics or for disinfection in anthrax outbreaks. In this study, two temperate B. anthracis phages, vB_BanS_A16R1 (A16R1) and vB_BanS_A16R4 (A16R4), were isolated and showed siphovirus-like morphological characteristics. Genome sequencing showed that the genomes of phages A16R1 and A16R4 are 36,569 bp and 40,059 bp in length, respectively. A16R1 belongs to the genus Wbetavirus, while A16R4 belongs to the genus Hubeivirus and is the first phage of that genus found to lyse B. anthracis. Because these two phages can comparatively specifically lyse B. anthracis, they could be used as alternative diagnostic tools for identification of B. anthracis infections.
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Affiliation(s)
- Lun Li
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
- School of Public Health, Dali University, Dali, China
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Huijuan Zhang
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Haixiao Jin
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Jin Guo
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Pan Liu
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Jiao Yang
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Zijian Wang
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Enmin Zhang
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Binbin Yu
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Liyuan Shi
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Jinrong He
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Peng Wang
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China
| | - Jianchun Wei
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China
| | - Youhong Zhong
- Yunnan Institute for Endemic Disease Control and Prevention, Dali, China.
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Dali, China.
| | - Wei Li
- National Institute for Communicable Disease Control and Prevention (ICDC), China CDC, Beijing, China.
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Beijing, China.
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Guo Z, Liu M, Zhang D. Potential of phage depolymerase for the treatment of bacterial biofilms. Virulence 2023; 14:2273567. [PMID: 37872768 PMCID: PMC10621286 DOI: 10.1080/21505594.2023.2273567] [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: 03/07/2023] [Accepted: 08/30/2023] [Indexed: 10/25/2023] Open
Abstract
Resistance of bacteria to antibiotics is a major concern in medicine and veterinary science. The bacterial biofilm structures not only prevent the penetration of drugs into cells within the biofilm's interior but also aid in evasion of the host immune system. Hence, there is an urgent need to develop novel therapeutic approaches against bacterial biofilms. One potential strategy to counter biofilms is to use phage depolymerases that degrade the matrix structure of the bacteria and enable access to bacterial cells. This review mainly discusses the methods by which phage depolymerases enhance the efficacy of the human immune system and the therapeutic applications of some phage depolymerases, such as single phage depolymerase application, combined therapy with phage depolymerase and antibiotics, and phage depolymerase cocktails, for treating bacterial biofilms. This review also summarizes the relationship between bacterial biofilms and antibiotic resistance.
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Affiliation(s)
- Zhimin Guo
- Department of Laboratory Medicine, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China
| | - Mengmeng Liu
- Department of Laboratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Dan Zhang
- Department of Hepatological Surgery, The First Hospital of Jilin University, Changchun, China
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Suresh S, Saldanha J, Bhaskar Shetty A, Premanath R, Akhila DS, Mohan Raj JR. Comparison of Antibiofilm Activity of Pseudomonas aeruginosa Phages on Isolates from Wounds of Diabetic and Non-Diabetic Patients. Microorganisms 2023; 11:2230. [PMID: 37764074 PMCID: PMC10536433 DOI: 10.3390/microorganisms11092230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Revised: 08/03/2023] [Accepted: 08/15/2023] [Indexed: 09/29/2023] Open
Abstract
The persistence of organisms as biofilms and the increase in antimicrobial resistance has raised the need for alternative strategies. The study objective was to compare the ability of isolated bacteriophages to remove in vitro biofilms formed by Pseudomonas aeruginosa isolated from the environment with those isolated from diabetic and non-diabetic wounds. P. aeruginosa were isolated from clinical and environmental sites, and antimicrobial susceptibility was tested. Bacteriophages were isolated and characterized based on plaque morphology and host range. A reduction in the viable count assayed the lytic ability of candidate phages. The crystal violet method was used to determine the residual biofilm after 24 h of phage treatment on 72-h-old biofilms. The statistical significance of phage treatment was tested by one-way ANOVA. Of 35 clinical isolates, 17 showed resistance to 1 antibiotic at least, and 7 were multidrug resistant. Nineteen environmental isolates and 11 clinical isolates were drug-sensitive. Nine phages showed 91.2% host coverage, including multidrug-resistant isolates. Phages eradicated 85% of biofilms formed by environmental isolates compared to 58% of biofilms of diabetic isolates and 56% of biofilms of non-diabetic isolates. Clinical isolates are susceptible to phage infection in planktonic form. Biofilms of P. aeruginosa isolated from diabetic wounds and non-diabetic wounds resist removal by phages compared to biofilms formed by environmental isolates. All phages were efficient in dispersing PAO1 biofilms. However, there was a significant difference in their ability to disperse PAO1 biofilms across the different surfaces tested. Partial eradication of biofilm by phages can aid in complementing antibiotics that are unable to penetrate biofilms in a clinical set-up.
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Affiliation(s)
| | | | | | | | | | - Juliet Roshini Mohan Raj
- Division of Infectious Diseases, Nitte University Center for Science Education and Research, Paneer Campus, Nitte (Deemed to be University), Derelakatte, Mangaluru 575018, India (R.P.); (D.S.A.)
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6
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Kauser A, Parisini E, Suarato G, Castagna R. Light-Based Anti-Biofilm and Antibacterial Strategies. Pharmaceutics 2023; 15:2106. [PMID: 37631320 PMCID: PMC10457815 DOI: 10.3390/pharmaceutics15082106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/29/2023] [Accepted: 08/02/2023] [Indexed: 08/27/2023] Open
Abstract
Biofilm formation and antimicrobial resistance pose significant challenges not only in clinical settings (i.e., implant-associated infections, endocarditis, and urinary tract infections) but also in industrial settings and in the environment, where the spreading of antibiotic-resistant bacteria is on the rise. Indeed, developing effective strategies to prevent biofilm formation and treat infections will be one of the major global challenges in the next few years. As traditional pharmacological treatments are becoming inadequate to curb this problem, a constant commitment to the exploration of novel therapeutic strategies is necessary. Light-triggered therapies have emerged as promising alternatives to traditional approaches due to their non-invasive nature, precise spatial and temporal control, and potential multifunctional properties. Here, we provide a comprehensive overview of the different biofilm formation stages and the molecular mechanism of biofilm disruption, with a major focus on the quorum sensing machinery. Moreover, we highlight the principal guidelines for the development of light-responsive materials and photosensitive compounds. The synergistic effects of combining light-triggered therapies with conventional treatments are also discussed. Through elegant molecular and material design solutions, remarkable results have been achieved in the fight against biofilm formation and antibacterial resistance. However, further research and development in this field are essential to optimize therapeutic strategies and translate them into clinical and industrial applications, ultimately addressing the global challenges posed by biofilm and antimicrobial resistance.
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Affiliation(s)
- Ambreen Kauser
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia; (A.K.); (E.P.)
- Faculty of Materials Science and Applied Chemistry, Riga Technical University, Paula Valdena 3, LV-1048 Riga, Latvia
| | - Emilio Parisini
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia; (A.K.); (E.P.)
- Department of Chemistry “G. Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Giulia Suarato
- Istituto di Elettronica e di Ingegneria dell’Informazione e delle Telecomunicazioni, Consiglio Nazionale delle Ricerche, CNR-IEIIT, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Rossella Castagna
- Department of Biotechnology, Latvian Institute of Organic Synthesis, Aizkraukles 21, LV-1006 Riga, Latvia; (A.K.); (E.P.)
- Dipartimento di Chimica, Materiali e Ingegneria Chimica “G. Natta”, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
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Shymialevich D, Wójcicki M, Świder O, Średnicka P, Sokołowska B. Characterization and Genome Study of a Newly Isolated Temperate Phage Belonging to a New Genus Targeting Alicyclobacillus acidoterrestris. Genes (Basel) 2023; 14:1303. [PMID: 37372483 DOI: 10.3390/genes14061303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 06/14/2023] [Accepted: 06/19/2023] [Indexed: 06/29/2023] Open
Abstract
The spoilage of juices by Alicyclobacillus spp. remains a serious problem in industry and leads to economic losses. Compounds such as guaiacol and halophenols, which are produced by Alicyclobacillus, create undesirable flavors and odors and, thus, decrease the quality of juices. The inactivation of Alicyclobacillus spp. constitutes a challenge because it is resistant to environmental factors, such as high temperatures, and active acidity. However, the use of bacteriophages seems to be a promising approach. In this study, we aimed to isolate and comprehensively characterize a novel bacteriophage targeting Alicyclobacillus spp. The Alicyclobacillus phage strain KKP 3916 was isolated from orchard soil against the Alicyclobacillus acidoterrestris strain KKP 3133. The bacterial host's range and the effect of phage addition at different rates of multiplicity of infections (MOIs) on the host's growth kinetics were determined using a Bioscreen C Pro growth analyzer. The Alicyclobacillus phage strain KKP 3916, retained its activity in a wide range of temperatures (from 4 °C to 30 °C) and active acidity values (pH from 3 to 11). At 70 °C, the activity of the phage decreased by 99.9%. In turn, at 80 °C, no activity against the bacterial host was observed. Thirty minutes of exposure to UV reduced the activity of the phages by almost 99.99%. Based on transmission-electron microscopy (TEM) and whole-genome sequencing (WGS) analyses, the Alicyclobacillus phage strain KKP 3916 was classified as a tailed bacteriophage. The genomic sequencing revealed that the newly isolated phage had linear double-stranded DNA (dsDNA) with sizes of 120 bp and 131 bp and 40.3% G+C content. Of the 204 predicted proteins, 134 were of unknown function, while the remainder were annotated as structural, replication, and lysis proteins. No genes associated with antibiotic resistance were found in the genome of the newly isolated phage. However, several regions, including four associated with integration into the bacterial host genome and excisionase, were identified, which indicates the temperate (lysogenic) life cycle of the bacteriophage. Due to the risk of its potential involvement in horizontal gene transfer, this phage is not an appropriate candidate for further research on its use in food biocontrol. To the best of our knowledge, this is the first article on the isolation and whole-genome analysis of the Alicyclobacillus-specific phage.
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Affiliation(s)
- Dziyana Shymialevich
- Culture Collection of Industrial Microorganisms-Microbiological Resources Center, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland
| | - Michał Wójcicki
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland
| | - Olga Świder
- Department of Food Safety and Chemical Analysis, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland
| | - Paulina Średnicka
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Wacław Dąbrowski Institute of Agricultural and Food Biotechnology-State Research Institute, Rakowiecka 36 Str., 02-532 Warsaw, Poland
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Wakinaka T, Matsutani M, Watanabe J, Mogi Y, Tokuoka M, Ohnishi A. Identification of Capsular Polysaccharide Synthesis Loci Determining Bacteriophage Susceptibility in Tetragenococcus halophilus. Microbiol Spectr 2023; 11:e0038523. [PMID: 37154759 PMCID: PMC10269466 DOI: 10.1128/spectrum.00385-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 04/17/2023] [Indexed: 05/10/2023] Open
Abstract
Bacteriophages infecting Tetragenococcus halophilus, a halophilic lactic acid bacterium, have been a major industrial concern due to their detrimental effects on the quality of food products. Previously characterized tetragenococcal phages displayed narrow host ranges, but there is little information on these mechanisms. Here, we revealed the host's determinant factors for phage susceptibility using two virulent phages, phiYA5_2 and phiYG2_4, that infect T. halophilus YA5 and YG2, respectively. Phage-resistant derivatives were obtained from these host strains, and mutations were found at the capsular polysaccharide (CPS) synthesis (cps) loci. Quantification analysis verified that capsular polysaccharide production by the cps derivatives from YG2 was impaired. Transmission electron microscopy observation confirmed the presence of filamentous structures outside the cell walls of YG2 and their absence in the cps derivatives of YG2. Phage adsorption assays revealed that phiYG2_4 adsorbed to YG2 but not its cps derivatives, which suggests that the capsular polysaccharide of YG2 is the specific receptor for phiYG2_4. Interestingly, phiYA5_2 adsorbed and infected cps derivatives of YG2, although neither adsorption to nor infection of the parental strain YG2 by phiYA5_2 was observed. The plaque-surrounding halos formed by phiYA5_2 implied the presence of the virion-associated depolymerase that degrades the capsular polysaccharide of YA5. These results indicated that the capsular polysaccharide is a physical barrier rather than a binding receptor for phiYA5_2 and that phiYA5_2 specifically overcomes the capsular polysaccharide of YA5. Thus, it is suggested that tetragenococcal phages utilize CPSs as binding receptors and/or degrade CPSs to approach host cells. IMPORTANCE T. halophilus is a halophilic lactic acid bacterium that contributes to the fermentation processes for various salted foods. Bacteriophage infections of T. halophilus have been a major industrial problem causing fermentation failures. Here, we identified the cps loci in T. halophilus as genetic determinants of phage susceptibility. The structural diversity of the capsular polysaccharide is responsible for the narrow host ranges of tetragenococcal phages. The information provided here could facilitate future studies on tetragenococcal phages and the development of efficient methods to prevent bacteriophage infections.
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Affiliation(s)
| | | | - Jun Watanabe
- Manufacturing Division, Yamasa Corporation, Choshi, Japan
- Faculty of Food and Agricultural Sciences, Fukushima University, Fukushima, Japan
- Institute of Fermentation Sciences, Fukushima University, Fukushima, Japan
| | - Yoshinobu Mogi
- Manufacturing Division, Yamasa Corporation, Choshi, Japan
| | - Masafumi Tokuoka
- Department of Fermentation Science, Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo, Japan
| | - Akihiro Ohnishi
- Department of Fermentation Science, Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo, Japan
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Chen Y, Li W, Shi K, Fang Z, Yang Y, Zhang R. Isolation and characterization of a novel phage belonging to a new genus against Vibrio parahaemolyticus. Virol J 2023; 20:81. [PMID: 37127579 PMCID: PMC10152775 DOI: 10.1186/s12985-023-02036-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 04/11/2023] [Indexed: 05/03/2023] Open
Abstract
BACKGROUND Vibrio parahaemolyticus is a major foodborne pathogen that contaminates aquatic products and causes great economic losses to aquaculture. Because of the emergence of multidrug-resistant V. parahaemolyticus strains, bacteriophages are considered promising agents for their biocontrol as an alternative or supplement to antibiotics. In this study, a lytic vibriophage, vB_VpaM_R16F (R16F), infecting V. parahaemolyticus 1.1997T was isolated, characterized and evaluated for its biocontrol potential. METHODS A vibriophage R16F was isolated from sewage from a seafood market with the double-layer agar method. R16F was studied by transmission electron microscopy, host range, sensitivity of phage particles to chloroform, one-step growth curve and lytic activity. The phage genome was sequenced and in-depth characterized, including phylogenetic and taxonomic analysis. RESULTS R16F belongs to the myovirus morphotype and infects V. parahaemolyticus, but not nine other Vibrio spp. As characterized by determining its host range, one-step growth curve, and lytic activity, phage R16F was found to highly effective in lysing host cells with a short latent period (< 10 min) and a small burst size (13 plaque-forming units). R16F has a linear double-stranded DNA with genome size 139,011 bp and a G + C content of 35.21%. Phylogenetic and intergenomic nucleotide sequence similarity analysis revealed that R16F is distinct from currently known vibriophages and belongs to a novel genus. Several genes (e.g., encoding ultraviolet damage endonuclease and endolysin) that may enhance environmental competitiveness were found in the genome of R16F, while no antibiotic resistance- or virulence factor-related gene was detected. CONCLUSIONS In consideration of its biological and genetic properties, this newly discovered phage R16F belongs to a novel genus and may be a potential alternate biocontrol agent.
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Affiliation(s)
- Yubing Chen
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, 43900, Selangor, Malaysia
| | - Wenqing Li
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China
| | - Keming Shi
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China
| | - Zheng Fang
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, 43900, Selangor, Malaysia
| | - Yunlan Yang
- State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen, 361102, Fujian, China.
- College of Ocean and Earth Sciences, Fujian Key Laboratory of Marine Carbon Sequestration, Xiamen University, Xiamen, 361102, Fujian, China.
| | - Rui Zhang
- Institute for Advanced Study, Shenzhen University, Shenzhen, 518061, Guangdong, China.
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Lammens EM, Feyaerts N, Kerremans A, Boon M, Lavigne R. Assessing the Orthogonality of Phage-Encoded RNA Polymerases for Tailored Synthetic Biology Applications in Pseudomonas Species. Int J Mol Sci 2023; 24:ijms24087175. [PMID: 37108338 PMCID: PMC10138996 DOI: 10.3390/ijms24087175] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 04/29/2023] Open
Abstract
The phage T7 RNA polymerase (RNAP) and lysozyme form the basis of the widely used pET expression system for recombinant expression in the biotechnology field and as a tool in microbial synthetic biology. Attempts to transfer this genetic circuitry from Escherichia coli to non-model bacterial organisms with high potential have been restricted by the cytotoxicity of the T7 RNAP in the receiving hosts. We here explore the diversity of T7-like RNAPs mined directly from Pseudomonas phages for implementation in Pseudomonas species, thus relying on the co-evolution and natural adaptation of the system towards its host. By screening and characterizing different viral transcription machinery using a vector-based system in P. putida., we identified a set of four non-toxic phage RNAPs from phages phi15, PPPL-1, Pf-10, and 67PfluR64PP, showing a broad activity range and orthogonality to each other and the T7 RNAP. In addition, we confirmed the transcription start sites of their predicted promoters and improved the stringency of the phage RNAP expression systems by introducing and optimizing phage lysozymes for RNAP inhibition. This set of viral RNAPs expands the adaption of T7-inspired circuitry towards Pseudomonas species and highlights the potential of mining tailored genetic parts and tools from phages for their non-model host.
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Affiliation(s)
- Eveline-Marie Lammens
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Nathalie Feyaerts
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Alison Kerremans
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Maarten Boon
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, KU Leuven, Kasteelpark Arenberg 21 Box 2462, 3001 Leuven, Belgium
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11
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Zhao A, Sun J, Liu Y. Understanding bacterial biofilms: From definition to treatment strategies. Front Cell Infect Microbiol 2023; 13:1137947. [PMID: 37091673 PMCID: PMC10117668 DOI: 10.3389/fcimb.2023.1137947] [Citation(s) in RCA: 31] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/09/2023] [Indexed: 04/08/2023] Open
Abstract
Bacterial biofilms are complex microbial communities encased in extracellular polymeric substances. Their formation is a multi-step process. Biofilms are a significant problem in treating bacterial infections and are one of the main reasons for the persistence of infections. They can exhibit increased resistance to classical antibiotics and cause disease through device-related and non-device (tissue) -associated infections, posing a severe threat to global health issues. Therefore, early detection and search for new and alternative treatments are essential for treating and suppressing biofilm-associated infections. In this paper, we systematically reviewed the formation of bacterial biofilms, associated infections, detection methods, and potential treatment strategies, aiming to provide researchers with the latest progress in the detection and treatment of bacterial biofilms.
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Affiliation(s)
- Ailing Zhao
- Department of Gastroenterology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, China
| | - Jiazheng Sun
- Department of Vasculocardiology, Jinzhou Medical University, Jinzhou, Liaoning, China
| | - Yipin Liu
- Department of Gastroenterology, Yantai Affiliated Hospital of Binzhou Medical University, Yantai, Shandong, China
- *Correspondence: Yipin Liu,
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12
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Tu Q, Pu M, Li Y, Wang Y, Li M, Song L, Li M, An X, Fan H, Tong Y. Acinetobacter Baumannii Phages: Past, Present and Future. Viruses 2023; 15:v15030673. [PMID: 36992382 PMCID: PMC10057898 DOI: 10.3390/v15030673] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/23/2023] [Accepted: 02/28/2023] [Indexed: 03/06/2023] Open
Abstract
Acinetobacter baumannii (A. baumannii) is one of the most common clinical pathogens and a typical multi-drug resistant (MDR) bacterium. With the increase of drug-resistant A. baumannii infections, it is urgent to find some new treatment strategies, such as phage therapy. In this paper, we described the different drug resistances of A. baumannii and some basic properties of A. baumannii phages, analyzed the interaction between phages and their hosts, and focused on A. baumannii phage therapies. Finally, we discussed the chance and challenge of phage therapy. This paper aims to provide a more comprehensive understanding of A. baumannii phages and theoretical support for the clinical application of A. baumannii phages.
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Affiliation(s)
- Qihang Tu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mingfang Pu
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yahao Li
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuer Wang
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Maochen Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Lihua Song
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Mengzhe Li
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Xiaoping An
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Huahao Fan
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Correspondence: (H.F.); (Y.T.)
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering (BAIC-SM), Beijing University of Chemical Technology, Beijing 100029, China
- Correspondence: (H.F.); (Y.T.)
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13
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Mohammadi M, Saffari M, Siadat SD, Hejazi SH, Shayestehpour M, Motallebi M, Eidi M. Isolation, characterization, therapeutic potency, and genomic analysis of a novel bacteriophage vB_KshKPC-M against carbapenemase-producing Klebsiella pneumoniae strains (CRKP) isolated from Ventilator-associated pneumoniae (VAP) infection of COVID-19 patients. Ann Clin Microbiol Antimicrob 2023; 22:18. [PMID: 36829156 PMCID: PMC9955523 DOI: 10.1186/s12941-023-00567-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 02/15/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a significant clinical problem, given the lack of therapeutic options. The CRKP strains have emerged as an essential worldwide healthcare issue during the last 10 years. Global expansion of the CRKP has made it a significant public health hazard. We must consider to novel therapeutic techniques. Bacteriophages are potent restorative cases against infections with multiple drug-resistant bacteria. The Phages offer promising prospects for the treatment of CRKP infections. OBJECTIVE In this study, a novel K. pneumoniae phage vB_KshKPC-M was isolated, characterized, and sequenced, which was able to infect and lyse Carbapenem-resistant K. pneumoniae host specifically. METHODS One hundred clinical isolates of K. pneumoniae were collected from patients with COVID-19 associated with ventilator-associated acute pneumonia hospitalized at Shahid Beheshti Hospital, Kashan, Iran, from 2020 to 2021. Initially, all samples were cultured, and bacterial isolates identified by conventional biochemical tests, and then the ureD gene was used by PCR to confirm the isolates. The Antibiotic susceptibility test in the disc diffusion method and Minimum inhibitory concentrations for Colistin was done and interpreted according to guidelines. Phenotypic and molecular methods determined the Carbapenem resistance of isolates. The blaKPC, blaNDM, and blaOXA-23 genes were amplified for this detection. Biofilm determination of CRKP isolates was performed using a quantitative microtiter plate (MTP) method. The phage was isolated from wastewater during the summer season at a specific position from Beheshti Hospital (Kashan, Iran). The sample was processed and purified against the bacterial host, a CRKP strain isolated from a patient suffering from COVID-19 pneumoniae and resistance to Colistin with high potency for biofilm production. This isolate is called Kp100. The separated phages were diluted and titration by the double overlay agar plaque assay. The separate Phage is concentrated with 10% PEG and stored at -80 °C until use. The phage host range was identified by the spot test method. The purified phage morphology was determined using a transmission electron microscope. The phage stability tests (pH and temperature) were analyzed. The effect of cationic ions on phage adsorption was evaluated. The optimal titer of bacteriophage was determined to reduce the concentration of the CRKP strain. One-step growth assays were performed to identify the purified phage burst's latent cycle and size. The SDS-PAGE was used for phage proteins analysis. Phage DNA was extracted by chloroform technique, and the whole genome of lytic phage was sequenced using Illumina HiSeq technology (Illumina, San Diego, CA). For quality assurance and preprocessing, such as trimming, Geneious Prime 2021.2.2 and Spades 3.9.0. The whole genome sequence of the lytic phage is linked to the GenBank database accession number. RASTtk-v1.073 was used to predict and annotate the ORFs. Prediction of ORF was performed using PHASTER software. ResFinder is used to assess the presence of antimicrobial resistance and virulence genes in the genome. The tRNAs can-SE v2.0.6 is used to determine the presence of tRNA in the genome. Linear genome comparisons of phages and visualization of coding regions were performed using Easyfig 2.2.3 and Mauve 2.4.0. Phage lifestyles were predicted using the program PHACTS. Phylogenetic analysis and amino acid sequences of phage core proteins, such as the major capsid protein. Phylogenies were reconstructed using the Neighbor-Joining method with 1000 bootstrap repeat. HHpred software was used to predict depolymerase. In this study, GraphPad Prism version 9.1 was used for the statistical analysis. Student's t-test was used to compare the sets and the control sets, and the significance level was set at P ≤ 0.05. RESULTS Phage vB_KshKPC-M is assigned to the Siphoviridae, order Caudovirales. It was identified as a linear double-stranded DNA phage of 54,378 bp with 50.08% G + C content, had a relatively broad host range (97.7%), a short latency of 20 min, and a high burst size of 260 PFU/cell, and was maintained stable at different pH (3-11) and temperature (45-65 °C). The vB_KshKPC-M genome contains 91 open-reading frames. No tRNA, antibiotic resistance, toxin, virulence-related genes, or lysogen-forming gene clusters were detected in the phage genome. Comparative genomic analysis revealed that phage vB_KshKPC-M has sequence similarity to the Klebsiella phages, phage 13 (NC_049844.1), phage Sushi (NC_028774.1), phage vB_KpnD_PeteCarol (OL539448.1) and phage PWKp14 (MZ634345.1). CONCLUSION The broad host range and antibacterial activity make it a promising candidate for future phage therapy applications. The isolated phage was able to lyse most of the antibiotic-resistant clinical isolates. Therefore, this phage can be used alone or as a phage mixture in future studies to control and inhibit respiratory infections caused by these bacteria, especially in treating respiratory infections caused by resistant strains in sick patients.
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Affiliation(s)
- Mehrdad Mohammadi
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Pezeshk Blvd, Qotbe Ravandi Blvd, Kashan, 8715973449, Iran.
| | - Mahmood Saffari
- Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Pezeshk Blvd, Qotbe Ravandi Blvd, Kashan, 8715973449, Iran.
| | - Seyed Davar Siadat
- grid.420169.80000 0000 9562 2611Tuberculosis and Pulmonary Research Department, Pasteur Institute of Iran, Tehran, Iran ,grid.420169.80000 0000 9562 2611Microbiology Research Center (MRC), Pasteur Institute of Iran, Tehran, Iran
| | - Seyed Hossein Hejazi
- grid.411036.10000 0001 1498 685XDepartment of Parasitology and Mycology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Mohammad Shayestehpour
- grid.444768.d0000 0004 0612 1049Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Pezeshk Blvd, Qotbe Ravandi Blvd, Kashan, 8715973449 Iran
| | - Mitra Motallebi
- grid.444768.d0000 0004 0612 1049Department of Microbiology and Immunology, Faculty of Medicine, Kashan University of Medical Sciences, Pezeshk Blvd, Qotbe Ravandi Blvd, Kashan, 8715973449 Iran
| | - Milad Eidi
- grid.412266.50000 0001 1781 3962Department of Medical Genetics, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
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Transcriptomics-Driven Characterization of LUZ100, a T7-like Pseudomonas Phage with Temperate Features. mSystems 2023; 8:e0118922. [PMID: 36794936 PMCID: PMC10134795 DOI: 10.1128/msystems.01189-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023] Open
Abstract
Autographiviridae is a diverse yet distinct family of bacterial viruses marked by a strictly lytic lifestyle and a generally conserved genome organization. Here, we characterized Pseudomonas aeruginosa phage LUZ100, a distant relative of type phage T7. LUZ100 is a podovirus with a limited host range which likely uses lipopolysaccharide (LPS) as a phage receptor. Interestingly, infection dynamics of LUZ100 indicated moderate adsorption rates and low virulence, hinting at temperate characteristics. This hypothesis was supported by genomic analysis, which showed that LUZ100 shares the conventional T7-like genome organization yet carries key genes associated with a temperate lifestyle. To unravel the peculiar characteristics of LUZ100, ONT-cappable-seq transcriptomics analysis was performed. These data provided a bird's-eye view of the LUZ100 transcriptome and enabled the discovery of key regulatory elements, antisense RNA, and transcriptional unit structures. The transcriptional map of LUZ100 also allowed us to identify new RNA polymerase (RNAP)-promoter pairs that can form the basis for biotechnological parts and tools for new synthetic transcription regulation circuitry. The ONT-cappable-seq data revealed that the LUZ100 integrase and a MarR-like regulator (proposed to be involved in the lytic/lysogeny decision) are actively cotranscribed in an operon. In addition, the presence of a phage-specific promoter transcribing the phage-encoded RNA polymerase raises questions on the regulation of this polymerase and suggests that it is interwoven with the MarR-based regulation. This transcriptomics-driven characterization of LUZ100 supports recent evidence that T7-like phages should not automatically be assumed to have a strictly lytic life cycle. IMPORTANCE Bacteriophage T7, considered the "model phage" of the Autographiviridae family, is marked by a strictly lytic life cycle and conserved genome organization. Recently, novel phages within this clade have emerged which display characteristics associated with a temperate life cycle. Screening for temperate behavior is of utmost importance in fields like phage therapy, where strictly lytic phages are generally required for therapeutic applications. In this study, we applied an omics-driven approach to characterize the T7-like Pseudomonas aeruginosa phage LUZ100. These results led to the identification of actively transcribed lysogeny-associated genes in the phage genome, pointing out that temperate T7-like phages are emerging more frequent than initially thought. In short, the combination of genomics and transcriptomics allowed us to obtain a better understanding of the biology of nonmodel Autographiviridae phages, which can be used to optimize the implementation of phages and their regulatory elements in phage therapy and biotechnological applications, respectively.
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15
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Elois MA, da Silva R, Pilati GVT, Rodríguez-Lázaro D, Fongaro G. Bacteriophages as Biotechnological Tools. Viruses 2023; 15:v15020349. [PMID: 36851563 PMCID: PMC9963553 DOI: 10.3390/v15020349] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/14/2023] [Accepted: 01/18/2023] [Indexed: 01/28/2023] Open
Abstract
Bacteriophages are ubiquitous organisms that can be specific to one or multiple strains of hosts, in addition to being the most abundant entities on the planet. It is estimated that they exceed ten times the total number of bacteria. They are classified as temperate, which means that phages can integrate their genome into the host genome, originating a prophage that replicates with the host cell and may confer immunity against infection by the same type of phage; and lytics, those with greater biotechnological interest and are viruses that lyse the host cell at the end of its reproductive cycle. When lysogenic, they are capable of disseminating bacterial antibiotic resistance genes through horizontal gene transfer. When professionally lytic-that is, obligately lytic and not recently descended from a temperate ancestor-they become allies in bacterial control in ecological imbalance scenarios; these viruses have a biofilm-reducing capacity. Phage therapy has also been advocated by the scientific community, given the uniqueness of issues related to the control of microorganisms and biofilm production when compared to other commonly used techniques. The advantages of using bacteriophages appear as a viable and promising alternative. This review will provide updates on the landscape of phage applications for the biocontrol of pathogens in industrial settings and healthcare.
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Affiliation(s)
- Mariana Alves Elois
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Raphael da Silva
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - Giulia Von Tönnemann Pilati
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
| | - David Rodríguez-Lázaro
- Microbiology Division, Faculty of Sciences, University of Burgos, 09001 Burgos, Spain
- Research Centre for Emerging Pathogens and Global Health, University of Burgos, 09001 Burgos, Spain
| | - Gislaine Fongaro
- Laboratory of Applied Virology, Department of Microbiology, Immunology and Parasitology, Federal University of Santa Catarina, Florianópolis 88040-900, Brazil
- Correspondence:
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16
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Genomic characterization and application of a novel bacteriophage STG2 capable of reducing planktonic and biofilm cells of Salmonella. Int J Food Microbiol 2023; 385:109999. [DOI: 10.1016/j.ijfoodmicro.2022.109999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/06/2022]
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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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [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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Shymialevich D, Wójcicki M, Wardaszka A, Świder O, Sokołowska B, Błażejak S. Application of Lytic Bacteriophages and Their Enzymes to Reduce Saprophytic Bacteria Isolated from Minimally Processed Plant-Based Food Products-In Vitro Studies. Viruses 2022; 15:9. [PMID: 36680050 PMCID: PMC9865725 DOI: 10.3390/v15010009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/16/2022] [Accepted: 12/18/2022] [Indexed: 12/24/2022] Open
Abstract
The aim of this study was to isolate phage enzymes and apply them in vitro for eradication of the dominant saprophytic bacteria isolated from minimally processed food. Four bacteriophages-two Enterobacter-specific and two Serratia-specific, which produce lytic enzymes-were used in this research. Two methods of phage enzyme isolation were tested, namely precipitation with acetone and ultracentrifugation. It was found that the number of virions could be increased almost 100 times due to the extension of the cultivation time (72 h). The amplification of phage particles and lytic proteins was dependent on the time of cultivation. Considering the influence of isolated enzymes on the growth kinetics of bacterial hosts, proteins isolated with acetone after 72-hour phage propagation exhibited the highest inhibitory effect. The reduction of bacteria count was dependent on the concentration of enzymes in the lysates. The obtained results indicate that phages and their lytic enzymes could be used in further research aiming at the improvement of microbiological quality and safety of minimally processed food products.
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Affiliation(s)
- Dziyana Shymialevich
- Culture Collection of Industrial Microorganisms—Microbiological Resources Center, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Michał Wójcicki
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Artur Wardaszka
- Laboratory of Biotechnology and Molecular Engineering, Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Olga Świder
- Department of Food Safety and Chemical Analysis, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Barbara Sokołowska
- Department of Microbiology, Prof. Waclaw Dabrowski Institute of Agricultural and Food Biotechnology—State Research Institute, Rakowiecka 36 Street, 02-532 Warsaw, Poland
| | - Stanisław Błażejak
- Department of Biotechnology and Food Microbiology, Institute of Food Sciences, Warsaw University of Life Sciences (WULS–SGGW), Nowoursynowska 166 Street, 02-776 Warsaw, Poland
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19
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Ouyang R, Costa AR, Cassidy CK, Otwinowska A, Williams VCJ, Latka A, Stansfeld PJ, Drulis-Kawa Z, Briers Y, Pelt DM, Brouns SJJ, Briegel A. High-resolution reconstruction of a Jumbo-bacteriophage infecting capsulated bacteria using hyperbranched tail fibers. Nat Commun 2022; 13:7241. [PMID: 36433970 PMCID: PMC9700779 DOI: 10.1038/s41467-022-34972-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 11/14/2022] [Indexed: 11/26/2022] Open
Abstract
The Klebsiella jumbo myophage ϕKp24 displays an unusually complex arrangement of tail fibers interacting with a host cell. In this study, we combine cryo-electron microscopy methods, protein structure prediction methods, molecular simulations, microbiological and machine learning approaches to explore the capsid, tail, and tail fibers of ϕKp24. We determine the structure of the capsid and tail at 4.1 Å and 3.0 Å resolution. We observe the tail fibers are branched and rearranged dramatically upon cell surface attachment. This complex configuration involves fourteen putative tail fibers with depolymerase activity that provide ϕKp24 with the ability to infect a broad panel of capsular polysaccharide (CPS) types of Klebsiella pneumoniae. Our study provides structural and functional insight into how ϕKp24 adapts to the variable surfaces of capsulated bacterial pathogens, which is useful for the development of phage therapy approaches against pan-drug resistant K. pneumoniae strains.
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Affiliation(s)
- Ruochen Ouyang
- grid.43169.390000 0001 0599 1243MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xianning West Road 28, Xi’an, 710049 China ,grid.5132.50000 0001 2312 1970Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Ana Rita Costa
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands ,grid.5292.c0000 0001 2097 4740Kavli Institute of Nanoscience, Delft, The Netherlands
| | - C. Keith Cassidy
- grid.4991.50000 0004 1936 8948Department of Biochemistry, University of Oxford, Oxford, UK
| | - Aleksandra Otwinowska
- grid.8505.80000 0001 1010 5103Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63-77, 51-148 Wroclaw, Poland
| | - Vera C. J. Williams
- grid.5132.50000 0001 2312 1970Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Agnieszka Latka
- grid.8505.80000 0001 1010 5103Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63-77, 51-148 Wroclaw, Poland ,grid.5342.00000 0001 2069 7798Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Phill J. Stansfeld
- grid.7372.10000 0000 8809 1613School of Life Sciences & Department of Chemistry, University of Warwick, Coventry, CV4 7AL UK
| | - Zuzanna Drulis-Kawa
- grid.8505.80000 0001 1010 5103Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63-77, 51-148 Wroclaw, Poland
| | - Yves Briers
- grid.5342.00000 0001 2069 7798Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000 Ghent, Belgium
| | - Daniël M. Pelt
- grid.5132.50000 0001 2312 1970Leiden Institute of Advanced Computer Science, Leiden University, Niels Bohrweg 1, 2333CA Leiden, The Netherlands
| | - Stan J. J. Brouns
- grid.5292.c0000 0001 2097 4740Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, The Netherlands ,grid.5292.c0000 0001 2097 4740Kavli Institute of Nanoscience, Delft, The Netherlands
| | - Ariane Briegel
- grid.5132.50000 0001 2312 1970Department of Microbial Sciences, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
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20
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Antibiofilm activity of a lytic Salmonella phage on different Salmonella enterica serovars isolated from broiler farms. Int Microbiol 2022; 26:205-217. [PMID: 36334144 PMCID: PMC10148789 DOI: 10.1007/s10123-022-00294-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 10/20/2022] [Accepted: 10/27/2022] [Indexed: 11/06/2022]
Abstract
AbstractBacteriophages have been mainly used in treating infections caused by planktonic bacterial cells in the veterinary sector. However, their applications as antibiofilm agents have received little attention. Accordingly, a previously isolated Salmonella infecting Siphoviridae phage was investigated for host range against 15 Salmonella enterica isolates (S. Cape, S. Gallinarum, 4 S. Enteritidis, 3 S. Montevideo, S. Uno, S. Oritamerin, S. Belgdam, S. Agona, S. Daula, and S. Aba) recovered from the litters of commercial broiler farms. All S. enterica isolates were examined for their biofilm activity using a microtiter plate assay and for adrA, csgD, and gcpA genes using conventional PCR. The phage efficacy against established biofilms produced by the selected seven S. enterica isolates (S. Gallinarum, S. Enteritidis, S. Montevideo, S. Uno, S. Oritamerin, S. Belgdam, and S. Agona) was assessed using microtiter plate assay and reverse transcriptase real-time PCR over different incubation times of 5 and 24 h. All S. enterica isolates were strong biofilm formers. Moreover, the phage effectively reduced the biofilm activity of the established S. enterica biofilms in the microtiter plate assay using the independent sample t-test (P < 0.050). Furthermore, the relative expression levels of csgD, gcpA, and adrA genes in the biofilm cells of S. enterica isolate after phage treatment were significantly up-regulated to variable degrees using the independent sample t-test (P < 0.050). In conclusion, the present study revealed the potential use of Salmonella phage in reducing established biofilms produced by S. enterica serovars isolated from broiler farms.
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21
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Bai J, Zhang F, Liang S, Chen Q, Wang W, Wang Y, Martín-Rodríguez AJ, Sjöling Å, Hu R, Zhou Y. Isolation and Characterization of vB_kpnM_17-11, a Novel Phage Efficient Against Carbapenem-Resistant Klebsiella pneumoniae. Front Cell Infect Microbiol 2022; 12:897531. [PMID: 35865823 PMCID: PMC9294173 DOI: 10.3389/fcimb.2022.897531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/03/2022] [Indexed: 11/13/2022] Open
Abstract
Phages and phage-encoded proteins exhibit promising prospects in the treatment of Carbapenem-Resistant Klebsiella pneumoniae (CRKP) infections. In this study, a novel Klebsiella pneumoniae phage vB_kpnM_17-11 was isolated and identified by using a CRKP host. vB_kpnM_17-11 has an icosahedral head and a retractable tail. The latent and exponential phases were 30 and 60 minutes, respectively; the burst size was 31.7 PFU/cell and the optimal MOI was 0.001. vB_kpnM_17-11 remained stable in a wide range of pH (4-8) and temperature (4-40°C). The genome of vB_kpnM_17-11 is 165,894 bp, double-stranded DNA (dsDNA), containing 275 Open Reading Frames (ORFs). It belongs to the family of Myoviridae, order Caudovirales, and has a close evolutionary relationship with Klebsiella phage PKO111. Sequence analysis showed that the 4530 bp orf022 of vB_kpnM_17-11 encodes a putative depolymerase. In vitro testing demonstrated that vB_kpnM_17-11 can decrease the number of K. pneumoniae by 105-fold. In a mouse model of infection, phage administration improved survival and reduced the number of K. pneumoniae in the abdominal cavity by 104-fold. In conclusion, vB_kpnM_17-11 showed excellent in vitro and in vivo performance against K. pneumoniae infection and constitutes a promising candidate for the development of phage therapy against CRKP.
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Affiliation(s)
- Jiawei Bai
- Department of Pathogen Biology, School of Basic Medicine, Public Center Experimental Technology of Pathogen Biology, Southwest Medical University, Luzhou, China
| | - Feiyang Zhang
- Department of Pathogen Biology, School of Basic Medicine, Public Center Experimental Technology of Pathogen Biology, Southwest Medical University, Luzhou, China
| | - Shuang Liang
- Department of Pathogen Biology, School of Basic Medicine, Public Center Experimental Technology of Pathogen Biology, Southwest Medical University, Luzhou, China
| | - Qiao Chen
- Department of Pathogen Biology, School of Basic Medicine, Public Center Experimental Technology of Pathogen Biology, Southwest Medical University, Luzhou, China
| | - Wei Wang
- Department of Pathogen Biology, School of Basic Medicine, Public Center Experimental Technology of Pathogen Biology, Southwest Medical University, Luzhou, China
| | - Ying Wang
- Department of Pathogen Biology, School of Basic Medicine, Public Center Experimental Technology of Pathogen Biology, Southwest Medical University, Luzhou, China
| | | | - Åsa Sjöling
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Solna, Sweden
| | - Renjing Hu
- Department of Laboratory Medicine, The Affiliated Wuxi No.2 People’s Hospital of Nanjing Medical University, Wuxi, China
- *Correspondence: Renjing Hu, ; Yingshun Zhou,
| | - Yingshun Zhou
- Department of Pathogen Biology, School of Basic Medicine, Public Center Experimental Technology of Pathogen Biology, Southwest Medical University, Luzhou, China
- *Correspondence: Renjing Hu, ; Yingshun Zhou,
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22
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Chang RYK, Nang SC, Chan HK, Li J. Novel antimicrobial agents for combating antibiotic-resistant bacteria. Adv Drug Deliv Rev 2022; 187:114378. [PMID: 35671882 DOI: 10.1016/j.addr.2022.114378] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 05/26/2022] [Accepted: 05/26/2022] [Indexed: 12/16/2022]
Abstract
Antibiotic therapy has become increasingly ineffective against bacterial infections due to the rise of resistance. In particular, ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) have caused life-threatening infections in humans and represent a major global health threat due to a high degree of antibiotic resistance. To respond to this urgent call, novel strategies are urgently needed, such as bacteriophages (or phages), phage-encoded enzymes, immunomodulators and monoclonal antibodies. This review critically analyses these promising antimicrobial therapies for the treatment of multidrug-resistant bacterial infections. Recent advances in these novel therapeutic strategies are discussed, focusing on preclinical and clinical investigations, as well as combinatorial approaches. In this 'Bad Bugs, No Drugs' era, novel therapeutic strategies can play a key role in treating deadly infections and help extend the lifetime of antibiotics.
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23
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Visnapuu A, Van der Gucht M, Wagemans J, Lavigne R. Deconstructing the Phage-Bacterial Biofilm Interaction as a Basis to Establish New Antibiofilm Strategies. Viruses 2022; 14:v14051057. [PMID: 35632801 PMCID: PMC9145820 DOI: 10.3390/v14051057] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 05/11/2022] [Accepted: 05/11/2022] [Indexed: 12/19/2022] Open
Abstract
The bacterial biofilm constitutes a complex environment that endows the bacterial community within with an ability to cope with biotic and abiotic stresses. Considering the interaction with bacterial viruses, these biofilms contain intrinsic defense mechanisms that protect against phage predation; these mechanisms are driven by physical, structural, and metabolic properties or governed by environment-induced mutations and bacterial diversity. In this regard, horizontal gene transfer can also be a driver of biofilm diversity and some (pro)phages can function as temporary allies in biofilm development. Conversely, as bacterial predators, phages have developed counter mechanisms to overcome the biofilm barrier. We highlight how these natural systems have previously inspired new antibiofilm design strategies, e.g., by utilizing exopolysaccharide degrading enzymes and peptidoglycan hydrolases. Next, we propose new potential approaches including phage-encoded DNases to target extracellular DNA, as well as phage-mediated inhibitors of cellular communication; these examples illustrate the relevance and importance of research aiming to elucidate novel antibiofilm mechanisms contained within the vast set of unknown ORFs from phages.
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24
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Sanchez BC, Heckmann ER, Green SI, Clark JR, Kaplan HB, Ramig RF, Muldrew KL, Hines-Munson C, Skelton F, Trautner BW, Maresso AW. Development of Phage Cocktails to Treat E. coli Catheter-Associated Urinary Tract Infection and Associated Biofilms. Front Microbiol 2022; 13:796132. [PMID: 35620093 PMCID: PMC9127763 DOI: 10.3389/fmicb.2022.796132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 04/04/2022] [Indexed: 11/16/2022] Open
Abstract
High rates of antimicrobial resistance and formation of biofilms makes treatment of Escherichia coli catheter-associated urinary tract infections (CAUTI) particularly challenging. CAUTI affect 1 million patients per year in the United States and are associated with morbidity and mortality, particularly as an etiology for sepsis. Phage have been proposed as a potential therapeutic option. Here, we report the development of phage cocktails that lyse contemporary E. coli strains isolated from the urine of patients with spinal cord injury (SCI) and display strong biofilm-forming properties. We characterized E. coli phage against biofilms in two in vitro CAUTI models. Biofilm viability was measured by an MTT assay that determines cell metabolic activity and by quantification of colony forming units. Nine phage decreased cell viability by >80% when added individually to biofilms of two E. coli strains in human urine. A phage cocktail comprising six phage lyses 82% of the strains in our E. coli library and is highly effective against young and old biofilms and against biofilms on silicon catheter materials. Using antibiotics together with our phage cocktail prevented or decreased emergence of E. coli resistant to phage in human urine. We created an anti-biofilm phage cocktail with broad host range against E. coli strains isolated from urine. These phage cocktails may have therapeutic potential against CAUTI.
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Affiliation(s)
- Belkys C. Sanchez
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Emmaline R. Heckmann
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Sabrina I. Green
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Justin R. Clark
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Heidi B. Kaplan
- Department of Microbiology and Molecular Genetics, McGovern Medical School, UTHealth Houston, Houston, TX, United States
| | - Robert F. Ramig
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States
| | - Kenneth L. Muldrew
- Department of Pathology and Immunology, Baylor College of Medicine, Houston, TX, United States,Pathology and Laboratory Medicine, Michael E. DeBakey VA Medical Center, Houston, TX, United States,Section of Infectious Diseases, Department of Medicine, Baylor College of Medicine, Houston, TX, United States
| | - Casey Hines-Munson
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States
| | - Felicia Skelton
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States,H. Ben Taub Department of Physical Medicine and Rehabilitation, Baylor College of Medicine, Houston, TX, United States
| | - Barbara W. Trautner
- Center for Innovations in Quality, Effectiveness and Safety, Michael E. DeBakey VA Medical Center, Houston, TX, United States,Department of Medicine and Surgery, Baylor College of Medicine, Houston, TX, United States,Center for Translational Research on Inflammatory Diseases, Michael E. DeBakey VA Medical Center, Houston, TX, United States
| | - Anthony W. Maresso
- Tailored Antibacterials and Innovative Laboratories for Phage (Φ) Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, United States,*Correspondence: Anthony W. Maresso,
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Bujak K, Decewicz P, Kitowicz M, Radlinska M. Characterization of Three Novel Virulent Aeromonas Phages Provides Insights into the Diversity of the Autographiviridae Family. Viruses 2022; 14:1016. [PMID: 35632757 PMCID: PMC9145550 DOI: 10.3390/v14051016] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/29/2022] [Accepted: 05/05/2022] [Indexed: 11/17/2022] Open
Abstract
In this study, we isolated and characterized three novel virulent Autographiviridae bacteriophages, vB_AspA_Bolek, vB_AspA_Lolek, and vB_AspA_Tola, which infect different Aeromonas strains. These three host-pathogen pairs were derived from the same sampling location-the arsenic-containing microbial mats of the Zloty Stok gold mine. Functional analysis showed they are psychrotolerant (4-25 °C), albeit with a much wider temperature range of propagation for the hosts (≤37 °C). Comparative genomic analyses revealed a high nucleotide and amino acid sequence similarity of vB_AspA_Bolek and vB_AspA_Lolek, with significant differences exclusively in the C-terminal region of their tail fibers, which might explain their host range discrimination. The protein-based phage network, together with a phylogenetic analysis of the marker proteins, allowed us to assign vB_AspA_Bolek and vB_AspA_Lolek to the Beijerinckvirinae and vB_AspA_Tola to the Colwellvirinae subfamilies, but as three novel species, due to their low nucleotide sequence coverage and identity with other known phage genomes. Global comparative analysis showed that the studied phages are also markedly different from most of the 24 Aeromonas autographiviruses known so far. Finally, this study provides in-depth insight into the diversity of the Autographiviridae phages and reveals genomic similarities between selected groups of this family as well as between autographiviruses and their relatives of other Caudoviricetes families.
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Affiliation(s)
| | | | | | - Monika Radlinska
- Department of Environmental Microbiology and Biotechnology, Faculty of Biology, Institute of Microbiology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland; (K.B.); (P.D.); (M.K.)
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26
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Chen X, Tang Q, Li X, Zheng X, Li P, Li M, Wu F, Xu Z, Lu R, Zhang W. Isolation, characterization, and genome analysis of bacteriophage P929 that could specifically lyase the KL19 capsular type of Klebsiella pneumoniae. Virus Res 2022; 314:198750. [DOI: 10.1016/j.virusres.2022.198750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 01/09/2023]
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27
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«Development of an anti- Acinetobacter baumannii biofilm phage cocktail: Genomic Adaptation to the Host». Antimicrob Agents Chemother 2022; 66:e0192321. [PMID: 35041503 DOI: 10.1128/aac.01923-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The need for alternatives to antibiotic therapy due to the emergence of multidrug resistant bacteria (MDR), such as the nosocomial pathogen Acinetobacter baumannii, has led to the recovery of phage therapy. In addition, phages can be combined in cocktails to increase the host range. In this study, the evolutionary mechanism of adaptation was utilized in order to develop a phage adapted to A. baumannii, named phage Ab105-2phiΔCI404ad, from a mutant lytic phage, Ab105-2phiΔCI, previously developed by our group. The whole genome sequence of phage Ab105-2phiΔCI404ad was determined, showing that four genomic rearrangements events occurred in the tail morphogenesis module affecting the ORFs encoding the host receptor binding sites. As a consequence of the genomic rearrangements, 10 ORFs were lost and four new ORFs were obtained, all encoding tail proteins; two inverted regions were also derived from these events. The adaptation process increased the host range of the adapted phage by almost three folds. In addition, a depolymerase-expressing phenotype, indicated by formation of a halo, which was not observed in the ancestral phage, was obtained in 81% of the infected strains. A phage cocktail was formed by combining this phage with the A. baumannii phage vB_AbaP_B3, known to express a depolymerase. Both the individual phages and the phage cocktail showed strong antimicrobial activity against 5 clinical strains and 1 reference strain of A. baumannii tested. However, in all cases resistance to the bacterial strains was also observed. The antibiofilm activity of the individual phages and the cocktail was assayed. The phage cocktail displayed strong antibiofilm activity.
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28
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Sjahriani T, Wasito EB, Tyasningsih W. The Analysis of OmpA and Rz/Rz1 of Lytic Bacteriophage from Surabaya, Indonesia. SCIENTIFICA 2021; 2021:7494144. [PMID: 35096434 PMCID: PMC8794686 DOI: 10.1155/2021/7494144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/28/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
A good strategy to conquer the Escherichia coli-cause food-borne disease could be bacteriophages. Porins are a type of β-barrel proteins with diffuse channels and OmpA, which has a role in hydrophilic transport, is the most frequent porin in E. coli; it was also chosen as the potential receptor of the phage. And the Rz/Rz1 was engaged in the breakup of the host bacterial external membrane. This study aimed to analyze the amino acid of OmpA and Rz/Rz1 of lytic bacteriophage from Surabaya, Indonesia. This study employed a sample of 8 bacteriophages from the previous study. The OmpA analysis method was mass spectrometry. Rz/Rz1 was analyzed using PCR, DNA sequencing, Expasy Translation, and Expasy ProtParam. The result obtained 10% to 29% sequence coverage of OmpA, carrying the ligand-binding site. The Rz/Rz1 gene shares a high percentage of 97.04% to 98.89% identities with the Siphoviridae isolate ctTwQ4, partial genome, and Myoviridae isolate cthRA4, partial genome. The Mann-Whitney statistical tests indicate the significant differences between Alanine, Aspartate, Glycine, Proline, Serine (p=0.011), Asparagine, Cysteine (p=0.009), Isoleucine (p=0.043), Lysine (p=0.034), Methionine (p=0.001), Threonine (p=0.018), and Tryptophan (p=0.007) of OmpA and Rz/Rz1. The conclusion obtained from this study is the fact that OmpA acts as Phage 1, Phage 2, Phage 3, Phage 5, and Phage 6 receptors for its peptide composition comprising the ligand binding site, and Rz/Rz1 participates in host bacteria lysis.
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Affiliation(s)
- Tessa Sjahriani
- Doctoral Program, Faculty of Medicine, Universitas Airlangga, Dr. Moestopo Road No. 47, Surabaya 60285, Indonesia
- Department of Microbiology, Faculty of Medicine, Universitas Malahayati, Pramuka Road No. 27, Bandar Lampung 35158, Indonesia
| | - Eddy Bagus Wasito
- Department of Microbiology, Faculty of Medicine, Universitas Airlangga, Dr. Moestopo Road No. 47, Surabaya 60285, Indonesia
| | - Wiwiek Tyasningsih
- Department of Microbiology, Faculty of Veterinary Medicine, Universitas Airlangga, C Campus, Mulyorejo Road, Surabaya 60115, Indonesia
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Rahimi-Midani A, Lee SW, Choi TJ. Potential Solutions Using Bacteriophages against Antimicrobial Resistant Bacteria. Antibiotics (Basel) 2021; 10:antibiotics10121496. [PMID: 34943708 PMCID: PMC8698741 DOI: 10.3390/antibiotics10121496] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/01/2023] Open
Abstract
Bacteriophages are viruses that specifically infect a bacterial host. They play a great role in the modern biotechnology and antibiotic-resistant microbe era. Since the discovery of phages, their application as a control agent has faced challenges that made antibiotics a better fit for combating pathogenic bacteria. Recently, with the novel sequencing technologies providing new insight into the nature of bacteriophages, their application has a second chance to be used. However, novel challenges need to be addressed to provide proper strategies for their practical application. This review focuses on addressing these challenges by initially introducing the nature of bacteriophages and describing the phage-host-dependent strategies for phage application. We also describe the effect of the long-term application of phages in natural environments and other bacterial communities. Overall, this review gathered crucial information for the future application of phages. We predict the use of phages will not be the only control strategy against pathogenic bacteria. Therefore, more studies must be done for low-risk control methods against antimicrobial-resistant bacteria.
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Affiliation(s)
- Aryan Rahimi-Midani
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea; (A.R.-M.); (S.-W.L.)
- Department of Microbiology, Pukyong National University, Busan 48513, Korea
| | - Seon-Woo Lee
- Department of Applied Bioscience, Dong-A University, Busan 49315, Korea; (A.R.-M.); (S.-W.L.)
| | - Tae-Jin Choi
- Department of Microbiology, Pukyong National University, Busan 48513, Korea
- Correspondence:
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Danis-Wlodarczyk KM, Wozniak DJ, Abedon ST. Treating Bacterial Infections with Bacteriophage-Based Enzybiotics: In Vitro, In Vivo and Clinical Application. Antibiotics (Basel) 2021; 10:1497. [PMID: 34943709 PMCID: PMC8698926 DOI: 10.3390/antibiotics10121497] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 12/14/2022] Open
Abstract
Over the past few decades, we have witnessed a surge around the world in the emergence of antibiotic-resistant bacteria. This global health threat arose mainly due to the overuse and misuse of antibiotics as well as a relative lack of new drug classes in development pipelines. Innovative antibacterial therapeutics and strategies are, therefore, in grave need. For the last twenty years, antimicrobial enzymes encoded by bacteriophages, viruses that can lyse and kill bacteria, have gained tremendous interest. There are two classes of these phage-derived enzymes, referred to also as enzybiotics: peptidoglycan hydrolases (lysins), which degrade the bacterial peptidoglycan layer, and polysaccharide depolymerases, which target extracellular or surface polysaccharides, i.e., bacterial capsules, slime layers, biofilm matrix, or lipopolysaccharides. Their features include distinctive modes of action, high efficiency, pathogen specificity, diversity in structure and activity, low possibility of bacterial resistance development, and no observed cross-resistance with currently used antibiotics. Additionally, and unlike antibiotics, enzybiotics can target metabolically inactive persister cells. These phage-derived enzymes have been tested in various animal models to combat both Gram-positive and Gram-negative bacteria, and in recent years peptidoglycan hydrolases have entered clinical trials. Here, we review the testing and clinical use of these enzymes.
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Affiliation(s)
| | - Daniel J. Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA;
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA;
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31
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Danis-Wlodarczyk KM, Cai A, Chen A, Gittrich MR, Sullivan MB, Wozniak DJ, Abedon ST. Friends or Foes? Rapid Determination of Dissimilar Colistin and Ciprofloxacin Antagonism of Pseudomonas aeruginosa Phages. Pharmaceuticals (Basel) 2021; 14:1162. [PMID: 34832944 PMCID: PMC8624478 DOI: 10.3390/ph14111162] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 11/10/2021] [Accepted: 11/11/2021] [Indexed: 12/14/2022] Open
Abstract
Phage therapy is a century-old technique employing viruses (phages) to treat bacterial infections, and in the clinic it is often used in combination with antibiotics. Antibiotics, however, interfere with critical bacterial metabolic activities that can be required by phages. Explicit testing of antibiotic antagonism of phage infection activities, though, is not a common feature of phage therapy studies. Here we use optical density-based 'lysis-profile' assays to assess the impact of two antibiotics, colistin and ciprofloxacin, on the bactericidal, bacteriolytic, and new-virion-production activities of three Pseudomonas aeruginosa phages. Though phages and antibiotics in combination are more potent in killing P. aeruginosa than either acting alone, colistin nevertheless substantially interferes with phage bacteriolytic and virion-production activities even at its minimum inhibitory concentration (1× MIC). Ciprofloxacin, by contrast, has little anti-phage impact at 1× or 3× MIC. We corroborate these results with more traditional measures, particularly colony-forming units, plaque-forming units, and one-step growth experiments. Our results suggest that ciprofloxacin could be useful as a concurrent phage therapy co-treatment especially when phage replication is required for treatment success. Lysis-profile assays also appear to be useful, fast, and high-throughput means of assessing antibiotic antagonism of phage infection activities.
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Affiliation(s)
| | - Alice Cai
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| | - Anna Chen
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| | - Marissa R. Gittrich
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| | - Matthew B. Sullivan
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
- Department of Civil, Environmental and Geodetic Engineering, The Ohio State University, Columbus, OH 43210, USA
| | - Daniel J. Wozniak
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH 43210, USA;
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
| | - Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA; (A.C.); (A.C.); (M.R.G.); (M.B.S.)
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Abedon ST, Danis-Wlodarczyk KM, Alves DR. Phage Therapy in the 21st Century: Is There Modern, Clinical Evidence of Phage-Mediated Efficacy? Pharmaceuticals (Basel) 2021; 14:1157. [PMID: 34832939 PMCID: PMC8625828 DOI: 10.3390/ph14111157] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 12/19/2022] Open
Abstract
Many bacteriophages are obligate killers of bacteria. That this property could be medically useful was first recognized over one hundred years ago, with 2021 being the 100-year anniversary of the first clinical phage therapy publication. Here we consider modern use of phages in clinical settings. Our aim is to answer one question: do phages serve as effective anti-bacterial infection agents when used clinically? An important emphasis of our analyses is on whether phage therapy-associated anti-bacterial infection efficacy can be reasonably distinguished from that associated with often coadministered antibiotics. We find that about half of 70 human phage treatment reports-published in English thus far in the 2000s-are suggestive of phage-mediated anti-bacterial infection efficacy. Two of these are randomized, double-blinded, infection-treatment studies while 14 of those studies, in our opinion, provide superior evidence of a phage role in observed treatment successes. Roughly three-quarters of these potentially phage-mediated outcomes are based on microbiological as well as clinical results, with the rest based on clinical success. Since many of these phage treatments are of infections for which antibiotic therapy had not been successful, their collective effectiveness is suggestive of a valid utility in employing phages to treat otherwise difficult-to-cure bacterial infections.
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Affiliation(s)
- Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA;
| | | | - Diana R. Alves
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA;
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Zhang Y, Liao YT, Salvador A, Lavenburg VM, Wu VCH. Characterization of Two New Shiga Toxin-Producing Escherichia coli O103-Infecting Phages Isolated from an Organic Farm. Microorganisms 2021; 9:microorganisms9071527. [PMID: 34361962 PMCID: PMC8303462 DOI: 10.3390/microorganisms9071527] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/12/2021] [Accepted: 07/12/2021] [Indexed: 01/21/2023] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) O103 strains have been recently attributed to various foodborne outbreaks in the United States. Due to the emergence of antibiotic-resistant strains, lytic phages are considered as alternative biocontrol agents. This study was to biologically and genomically characterize two STEC O103-infecting bacteriophages, vB_EcoP-Ro103C3lw (or Ro103C3lw) and vB_EcoM-Pr103Blw (or Pr103Blw), isolated from an organic farm. Based on genomic and morphological analyses, phages Ro103C3lw and Pr103Blw belonged to Autographiviridae and Myoviridae families, respectively. Ro103C3lw contained a 39,389-bp double-stranded DNA and encoded a unique tail fiber with depolymerase activity, resulting in huge plaques. Pr103Blw had an 88,421-bp double-stranded DNA with 26 predicted tRNAs associated with the enhancement of the phage fitness. Within each phage genome, no virulence, antibiotic-resistant, and lysogenic genes were detected. Additionally, Ro103C3lw had a short latent period (2 min) and a narrow host range, infecting only STEC O103 strains. By contrast, Pr103Blw had a large burst size (152 PFU/CFU) and a broad host range against STEC O103, O26, O111, O157:H7, and Salmonella Javiana strains. Furthermore, both phages showed strong antimicrobial activities against STEC O103:H2 strains. The findings provide valuable insight into these two phages’ genomic features with the potential antimicrobial activities against STEC O103.
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Ma R, Lai J, Chen X, Wang L, Yang Y, Wei S, Jiao N, Zhang R. A Novel Phage Infecting Alteromonas Represents a Distinct Group of Siphophages Infecting Diverse Aquatic Copiotrophs. mSphere 2021; 6:e0045421. [PMID: 34106770 PMCID: PMC8265664 DOI: 10.1128/msphere.00454-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 12/14/2022] Open
Abstract
Bacteriophages play critical roles in impacting microbial community succession both ecologically and evolutionarily. Although the majority of phage genetic diversity has been increasingly unveiled, phages infecting members of the ecologically important genus Alteromonas remain poorly understood. Here, we present a comprehensive analysis of a newly isolated alterophage, vB_AcoS-R7M (R7M), to characterize its life cycle traits, genomic features, and putative evolutionary origin. R7M harbors abundant genes identified as host-like auxiliary metabolic genes facilitating viral propagation. Genomic analysis suggested that R7M is distinct from currently known alterophages. Interestingly, R7M was found to share a set of similar characteristics with a number of siphophages infecting diverse aquatic opportunistic copiotrophs. We therefore proposed the creation of one new subfamily (Queuovirinae) to group with these evolutionarily related phages. Notably, tail genes were less likely to be shared among them, and baseplate-related genes varied the most. In-depth analyses indicated that R7M has replaced its distal tail with a Rhodobacter capsulatus gene transfer agent (RcGTA)-like baseplate and further acquired a putative receptor interaction site targeting Alteromonas. These findings suggest that horizontal exchanges of viral tail adsorption apparatuses are widespread and vital for phages to hunt new hosts and to adapt to new niches. IMPORTANCE The evolution and ecology of phages infecting members of Alteromonas, a marine opportunistic genus that is widely distributed and of great ecological significance, remain poorly understood. The present study integrates physiological and genomic evidence to characterize the properties and putative phage-host interactions of a newly isolated Alteromonas phage, vB_AcoS-R7M (R7M). A taxonomic study reveals close evolutionary relationships among R7M and a number of siphophages infecting various aquatic copiotrophs. Their similar head morphology and overall genetic framework suggest their putative common ancestry and the grouping of a new viral subfamily. However, their major difference lies in the viral tail adsorption apparatuses and the horizontal exchanges of which possibly account for variations in host specificity. These findings outline an evolutionary scenario for the emergence of diverse viral lineages of a shared genetic pool and give insights into the genetics and ecology of viral host jumps.
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Affiliation(s)
- Ruijie Ma
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Jiayong Lai
- College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Xiaowei Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Long Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
| | - Yahui Yang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Shuzhen Wei
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Rui Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, China
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Improving Phage-Biofilm In Vitro Experimentation. Viruses 2021; 13:v13061175. [PMID: 34205417 PMCID: PMC8234374 DOI: 10.3390/v13061175] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 02/07/2023] Open
Abstract
Bacteriophages or phages, the viruses of bacteria, are abundant components of most ecosystems, including those where bacteria predominantly occupy biofilm niches. Understanding the phage impact on bacterial biofilms therefore can be crucial toward understanding both phage and bacterial ecology. Here, we take a critical look at the study of bacteriophage interactions with bacterial biofilms as carried out in vitro, since these studies serve as bases of our ecological and therapeutic understanding of phage impacts on biofilms. We suggest that phage-biofilm in vitro experiments often may be improved in terms of both design and interpretation. Specific issues discussed include (a) not distinguishing control of new biofilm growth from removal of existing biofilm, (b) inadequate descriptions of phage titers, (c) artificially small overlying fluid volumes, (d) limited explorations of treatment dosing and duration, (e) only end-point rather than kinetic analyses, (f) importance of distinguishing phage enzymatic from phage bacteriolytic anti-biofilm activities, (g) limitations of biofilm biomass determinations, (h) free-phage interference with viable-count determinations, and (i) importance of experimental conditions. Toward bettering understanding of the ecology of bacteriophage-biofilm interactions, and of phage-mediated biofilm disruption, we discuss here these various issues as well as provide tips toward improving experiments and their reporting.
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Engineering the Modular Receptor-Binding Proteins of Klebsiella Phages Switches Their Capsule Serotype Specificity. mBio 2021; 12:mBio.00455-21. [PMID: 33947754 PMCID: PMC8262889 DOI: 10.1128/mbio.00455-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The high specificity of bacteriophages is driven by their receptor-binding proteins (RBPs). Many Klebsiella bacteriophages target the capsular exopolysaccharide as the receptor and encode RBPs with depolymerase activity. The modular structure of these RBPs with an N-terminal structural module to attach the RBP to the phage tail, and a C-terminal specificity module for exopolysaccharide degradation, supports horizontal transfer as a major evolutionary driver for Klebsiella phage RBPs. We mimicked this natural evolutionary process by the construction of modular RBP chimeras, exchanging N-terminal structural modules and C-terminal specificity modules. All chimeras strictly follow the capsular serotype specificity of the C-terminal module. Transplanting chimeras with a K11 N-terminal structural RBP module in a Klebsiella phage K11 scaffold results in a capsular serotype switch and corresponding host range modification of the synthetic phages, demonstrating that horizontal transfer of C-terminal specificity modules offers Klebsiella phages an evolutionary highway for rapid adaptation to new capsular serotypes.
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37
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De Smet J, Wagemans J, Hendrix H, Staes I, Visnapuu A, Horemans B, Aertsen A, Lavigne R. Bacteriophage-mediated interference of the c-di-GMP signalling pathway in Pseudomonas aeruginosa. Microb Biotechnol 2021; 14:967-978. [PMID: 33314648 PMCID: PMC8085984 DOI: 10.1111/1751-7915.13728] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/19/2020] [Accepted: 11/22/2020] [Indexed: 01/10/2023] Open
Abstract
C-di-GMP is a key signalling molecule which impacts bacterial motility and biofilm formation and is formed by the condensation of two GTP molecules by a diguanylate cyclase. We here describe the identification and characterization of a family of bacteriophage-encoded peptides that directly impact c-di-GMP signalling in Pseudomonas aeruginosa. These phage proteins target Pseudomonas diguanylate cyclase YfiN by direct protein interaction (termed YIPs, YfiN Interacting Peptides). YIPs induce an increase of c-di-GMP production in the host cell, resulting in a decrease in motility and an increase in biofilm mass in P. aeruginosa. A dynamic analysis of the biofilm morphology indicates a denser biofilm structure after induction of the phage protein. This intracellular signalling interference strategy by a lytic phage constitutes an unexplored phage-based mechanism of metabolic regulation and could potentially serve as inspiration for the development of molecules that interfere with biofilm formation in P. aeruginosa and other pathogens.
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Affiliation(s)
- Jeroen De Smet
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
- Present address:
Lab4FoodDepartment of Microbial and Molecular Systems (M2S)KU Leuven Campus GeelGeel2440Belgium
| | - Jeroen Wagemans
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
| | - Hanne Hendrix
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
| | - Ines Staes
- Laboratory of Food MicrobiologyDepartment of Microbial and Molecular SystemsKU LeuvenHeverlee3001Belgium
| | - Annegrete Visnapuu
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
| | - Benjamin Horemans
- Department of Earth and Environmental SciencesKU LeuvenHeverlee3001Belgium
| | - Abram Aertsen
- Laboratory of Food MicrobiologyDepartment of Microbial and Molecular SystemsKU LeuvenHeverlee3001Belgium
| | - Rob Lavigne
- Laboratory of Gene TechnologyDepartment of BiosystemsKU LeuvenHeverlee3001Belgium
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38
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Phage Biocontrol of Bacterial Leaf Blight Disease on Welsh Onion Caused by Xanthomonas axonopodis pv. allii. Antibiotics (Basel) 2021; 10:antibiotics10050517. [PMID: 34062921 PMCID: PMC8147253 DOI: 10.3390/antibiotics10050517] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/26/2021] [Accepted: 04/28/2021] [Indexed: 02/06/2023] Open
Abstract
Bacterial leaf blight, which is caused by Xanthomonas axonopodis pv. allii, annually causes significant yield losses to Welsh onion in many producing countries, including Vietnam. In this study, we isolated and characterized lytic phages Φ16, Φ17A and Φ31, specific to X. axonopodis pv. allii and belonging to a new phage species and genus within the Autographiviridae, from four provinces in the Mekong Delta of Vietnam. Moreover, we evaluated their efficacy for the biocontrol of leaf blight in greenhouse and field conditions. When applying the three highly related phages individually or as a three-phage cocktail at 108 PFU/mL in greenhouse conditions, our results show that treatment with Φ31 alone provides higher disease prevention than the two other phages or the phage cocktail. Furthermore, we compared phage concentrations from 105 to 108 and showed optimal disease control at 107 and 108 PFU/mL. Finally, under field conditions, both phage Φ31 alone and the phage cocktail treatments suppressed disease symptoms, which was comparable to the chemical bactericide oxolinic acid (Starner). Phage treatment also significantly improved yield, showing the potential of phage as a biocontrol strategy for managing leaf blight in Welsh onion.
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Hemmati F, Rezaee MA, Ebrahimzadeh S, Yousefi L, Nouri R, Kafil HS, Gholizadeh P. Novel Strategies to Combat Bacterial Biofilms. Mol Biotechnol 2021; 63:569-586. [PMID: 33914260 DOI: 10.1007/s12033-021-00325-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Accepted: 04/09/2021] [Indexed: 12/15/2022]
Abstract
Biofilms are considered as a severe problem in the treatment of bacterial infections; their development causes some noticeable resistance to antibacterial agents. Biofilms are responsible for at least two-thirds of all infections, displaying promoted resistance to classical antibiotic treatments. Therefore, finding new alternative therapeutic approaches is essential for the treatment and inhibition of biofilm-related infections. Therefore, this review aims to describe the potential therapeutic strategies that can inhibit bacterial biofilm development; these include the usage of antiadhesion agents, AMPs, bacteriophages, QSIs, aptamers, NPs and PNAs, which can prevent or eradicate the formation of biofilms. These antibiofilm agents represent a promising therapeutic target in the treatment of biofilm infections and development of a strong capability to interfere with different phases of the biofilm development, including adherence, polysaccharide intercellular adhesion (PIA), quorum sensing molecules and cell-to-cell connection, bacterial aggregation, planktonic bacteria killing and host-immune response modulation. In addition, these components, in combination with antibiotics, can lead to the development of some kind of powerful combined therapy against bacterial biofilm-related infections.
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Affiliation(s)
- Fatemeh Hemmati
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Saba Ebrahimzadeh
- Department of Food Science and Technology, Faculty of Agriculture and Natural Resources, Urmia University, Urmia, Iran
| | - Leila Yousefi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Roghayeh Nouri
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran.,Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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40
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Islam MS, Yang X, Euler CW, Han X, Liu J, Hossen MI, Zhou Y, Li J. Application of a novel phage ZPAH7 for controlling multidrug-resistant Aeromonas hydrophila on lettuce and reducing biofilms. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107785] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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41
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Žukauskienė E, Šimoliūnienė M, Truncaitė L, Skapas M, Kaupinis A, Valius M, Meškys R, Šimoliūnas E. Pantoea Bacteriophage vB_PagS_AAS23: A Singleton of the Genus Sauletekiovirus. Microorganisms 2021; 9:668. [PMID: 33807116 PMCID: PMC8004638 DOI: 10.3390/microorganisms9030668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
A cold-adapted siphovirus, vB_PagS_AAS23 (AAS23) was isolated in Lithuania using the Pantoea agglomerans strain AUR for the phage propagation. The double-stranded DNA genome of AAS23 (51,170 bp) contains 92 probable protein encoding genes, and no genes for tRNA. A comparative sequence analysis revealed that 25 of all AAS23 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. Based on the phylogenetic analysis, AAS23 has no close relationship to other viruses publicly available to date and represents a single species of the genus Sauletekiovirus within the family Drexlerviridae. The phage is able to form plaques in bacterial lawns even at 4 °C and demonstrates a depolymerase activity. Thus, the data presented in this study not only provides the information on Pantoea-infecting bacteriophages, but also offers novel insights into the diversity of cold-adapted viruses and their potential to be used as biocontrol agents.
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Affiliation(s)
- Emilija Žukauskienė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Monika Šimoliūnienė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Lidija Truncaitė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Martynas Skapas
- Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania;
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Rolandas Meškys
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Eugenijus Šimoliūnas
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
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Zurabov F, Zhilenkov E. Characterization of four virulent Klebsiella pneumoniae bacteriophages, and evaluation of their potential use in complex phage preparation. Virol J 2021; 18:9. [PMID: 33407669 PMCID: PMC7789013 DOI: 10.1186/s12985-020-01485-w] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 12/28/2020] [Indexed: 12/22/2022] Open
Abstract
Background Nowadays, hundreds of thousands of deaths per year are caused by antibiotic resistant nosocomial infections and the prognosis for future years is much worse, as evidenced by modern research. Bacteria of the Klebsiella genus are one of the main pathogens that cause nosocomial infections. Among the many antimicrobials offered to replace or supplement traditional antibiotics, bacteriophages are promising candidates. Methods This article presents microbiological, physicochemical and genomic characterization of 4 virulent bacteriophages belonging to Siphoviridae, Myoviridae and Podoviridae families. Phages were studied by electron microscopy; their host range, lytic activity, adsorption rate, burst size, latent period, frequency of phage-resistant forms generation, lysis dynamics and sensitivity of phage particles to temperature and pH were identified; genomes of all 4 bacteriophages were studied by restriction digestion and complete genome sequence. Results Studied phages showed wide host range and high stability at different temperature and pH values. In contrast with single phages, a cocktail of bacteriophages lysed all studied bacterial strains, moreover, no cases of the emergence of phage-resistant bacterial colonies were detected. Genomic data proved that isolated viruses do not carry antibiotic resistance, virulence or lysogenic genes. Three out of four bacteriophages encode polysaccharide depolymerases, which are involved in the degradation of biofilms and capsules. Conclusions The bacteriophages studied in this work are promising for further in vivo studies and might be used in phage therapy as part of a complex therapeutic and prophylactic phage preparation. The conducted studies showed that the complex preparation is more effective than individual phages. The use of the complex phage cocktail allows to extend the lytic spectrum, and significantly reduces the possibility of phage-resistant forms generation.
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Affiliation(s)
- Fedor Zurabov
- Research and Production Center "MicroMir", LLC, Moscow, Russia. .,Department of Virology, Lomonosov Moscow State University, Moscow, Russia.
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43
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Vukotic G, Obradovic M, Novovic K, Di Luca M, Jovcic B, Fira D, Neve H, Kojic M, McAuliffe O. Characterization, Antibiofilm, and Depolymerizing Activity of Two Phages Active on Carbapenem-Resistant Acinetobacter baumannii. Front Med (Lausanne) 2020; 7:426. [PMID: 32974360 PMCID: PMC7461965 DOI: 10.3389/fmed.2020.00426] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/01/2020] [Indexed: 01/21/2023] Open
Abstract
Acinetobacter baumannii is a leading cause of healthcare-associated infections worldwide. Its various intrinsic and acquired mechanisms of antibiotic resistance make the therapeutic challenge even more serious. One of the promising alternative treatments that is increasingly highlighted is phage therapy, the therapeutic use of bacteriophages to treat bacterial infections. Two phages active against nosocomial carbapenem-resistant A. baumannii strain 6077/12, vB_AbaM_ISTD, and vB_AbaM_NOVI, were isolated from Belgrade wastewaters, purified, and concentrated using CsCl gradient ultracentrifugation. The phages were screened against 103 clinical isolates of A. baumannii from a laboratory collection and characterized based on plaque and virion morphology, host range, adsorption rate, and one-step growth curve. Given that phage ISTD showed a broader host range, better adsorption rate, shorter latent period, and larger burst size, its ability to lyse planktonic and biofilm-embedded cells was tested in detail. Phage ISTD yielded a 3.5- and 2-log reduction in planktonic and biofilm-associated viable bacterial cell count, respectively, but the effect was time-dependent. Both phages produced growing turbid halos around plaques indicating the synthesis of depolymerases, enzymes capable of degrading bacterial exopolysaccharides. Halos tested positive for presence of phages in the proximity of the plaque, but not further from the plaque, which indicates that the observed halo enlargement is a consequence of enzyme diffusion through the agar, independently of the phages. This notion was also supported by the growing halos induced by phage preparations applied on pregrown bacterial lawns, indicating that depolymerizing effect was achieved also on non-dividing sensitive cells. Overall, good rates of growth, fast adsorption rate, broad host range, and high depolymerizing activity, as well as antibacterial effectiveness against planktonic and biofilm-associated bacteria, make these phages good candidates for potential application in combating A. baumannii infections.
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Affiliation(s)
- Goran Vukotic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.,Chair of Biochemistry and Molecular Biology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Mina Obradovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Katarina Novovic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | | | - Branko Jovcic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia.,Chair of Biochemistry and Molecular Biology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Djordje Fira
- Chair of Biochemistry and Molecular Biology, Faculty of Biology, University of Belgrade, Belgrade, Serbia
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Kiel, Germany
| | - Milan Kojic
- Laboratory for Molecular Microbiology, Institute of Molecular Genetics and Genetic Engineering, University of Belgrade, Belgrade, Serbia
| | - Olivia McAuliffe
- Department of Food Biosciences, Teagasc Food Research Centre, Fermoy, Ireland
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44
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Lelchat F, Mocaer PY, Ojima T, Michel G, Sarthou G, Bucciarelli E, Cérantola S, Colliec-Jouault S, Boisset C, Baudoux AC. Viral degradation of marine bacterial exopolysaccharides. FEMS Microbiol Ecol 2020; 95:5498295. [PMID: 31125051 DOI: 10.1093/femsec/fiz079] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/23/2019] [Indexed: 11/14/2022] Open
Abstract
The identification of the mechanisms by which marine dissolved organic matter (DOM) is produced and regenerated is critical to develop robust prediction of ocean carbon cycling. Polysaccharides represent one of the main constituents of marine DOM and their degradation is mainly attributed to polysaccharidases derived from bacteria. Here, we report that marine viruses can depolymerize the exopolysaccharides (EPS) excreted by their hosts using five bacteriophages that infect the notable EPS producer, Cobetia marina DSMZ 4741. Degradation monitorings as assessed by gel electrophoresis and size exclusion chromatography showed that four out of five phages carry structural enzymes that depolymerize purified solution of Cobetia marina EPS. The depolymerization patterns suggest that these putative polysaccharidases are constitutive, endo-acting and functionally diverse. Viral adsorption kinetics indicate that the presence of these enzymes provides a significant advantage for phages to adsorb onto their hosts upon intense EPS production conditions. The experimental demonstration that marine phages can display polysaccharidases active on bacterial EPS lead us to question whether viruses could also contribute to the degradation of marine DOM and modify its bioavailability. Considering the prominence of phages in the ocean, such studies may unveil an important microbial process that affects the marine carbon cycle.
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Affiliation(s)
- F Lelchat
- Laboratoire BMM, centre Ifremer de Brest, ZI pointe du diable, 29280 Plouzané, France
| | - P Y Mocaer
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
| | - T Ojima
- Laboratory of Marine Biotechnology and Microbiology, Graduate School of Fisheries Sciences, Hokkaido University, Minato-cho 3-1-1, Hakodate 041-8611, Japan
| | - G Michel
- Sorbonne Université, CNRS, Laboratoire de Biologie Intégrative des Modèles Marins UMR 8227, Station Biologique de Roscoff, Roscoff, France
| | - G Sarthou
- CNRS, Université de Brest, IRD, Ifremer, UMR 6539/LEMAR/IUEM, Technopôle Brest Iroise, Place Nicolas Copernic, 29280 Plouzané, France
| | - E Bucciarelli
- CNRS, Université de Brest, IRD, Ifremer, UMR 6539/LEMAR/IUEM, Technopôle Brest Iroise, Place Nicolas Copernic, 29280 Plouzané, France
| | - S Cérantola
- Service commun de résonnance magnétique nucléaire, Faculté de science de Brest, Université de Bretagne Occidentale, 6 av. Victor Le Gorgeu, 29238 Brest Cedex 3, France
| | - S Colliec-Jouault
- Laboratoire EM3B, Centre Ifremer Atlantique - Rue de l'Ile d'Yeu - 44311 Nantes, France
| | - C Boisset
- Service commun de chromatographie, CERMAV-CNRS, 601 rue de la chimie, St Martin d'Hère, 38041 Grenoble, France
| | - A-C Baudoux
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Station Biologique de Roscoff, Roscoff, France
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45
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Ferriol-González C, Domingo-Calap P. Phages for Biofilm Removal. Antibiotics (Basel) 2020; 9:antibiotics9050268. [PMID: 32455536 PMCID: PMC7277876 DOI: 10.3390/antibiotics9050268] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 05/15/2020] [Accepted: 05/19/2020] [Indexed: 12/21/2022] Open
Abstract
Biofilms are clusters of bacteria that live in association with surfaces. Their main characteristic is that the bacteria inside the biofilms are attached to other bacterial cells and to the surface by an extracellular polymeric matrix. Biofilms are capable of adhering to a wide variety of surfaces, both biotic and abiotic, including human tissues, medical devices, and other materials. On these surfaces, biofilms represent a major threat causing infectious diseases and economic losses. In addition, current antibiotics and common disinfectants have shown limited ability to remove biofilms adequately, and phage-based treatments are proposed as promising alternatives for biofilm eradication. This review analyzes the main advantages and challenges that phages can offer for the elimination of biofilms, as well as the most important factors to be taken into account in order to design effective phage-based treatments.
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Affiliation(s)
| | - Pilar Domingo-Calap
- Department of Genetics, Universitat de València, 46100 Valencia, Spain;
- Institute for Integrative Systems Biology, ISysBio, Universitat de València-CSIC, 46910 Valencia, Spain
- Correspondence: ; Tel.: +34-963-543-261
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46
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Isolation and application of bacteriophages alone or in combination with nisin against planktonic and biofilm cells of Staphylococcus aureus. Appl Microbiol Biotechnol 2020; 104:5145-5158. [PMID: 32248441 DOI: 10.1007/s00253-020-10581-4] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 03/14/2020] [Accepted: 03/23/2020] [Indexed: 01/02/2023]
Abstract
Staphylococcus aureus is a notorious foodborne pathogen since it has ability to produce variety of toxins including heat-stable enterotoxin, form biofilm, and acquire resistance to antibiotics. Biocontrol of foodborne pathogens by lytic bacteriophages garners increasing interest from both researchers and food industry. In the present study, 29 phages against S. aureus were successfully isolated from chicken, pork, and fish. Characterization of the isolates revealed that phage SA46-CTH2 belonging to Podoviridae family had a number of features suitable for food industry applications such as wide host range, short latent period, large burst size, high stress tolerance, and a genome free of virulence genes. Furthermore, phage SA46-CTH2 alone or in combination with nisin exhibited great efficacy in reducing planktonic and biofilm cells of S. aureus at various conditions tested. The combination of phage SA46-CTH2 and nisin was also found to be able to inhibit the regrowth of S. aureus at both 37 and 24 °C.Key points• A total of 29 S. aureus phages were successfully isolated from fish, pork, and chicken products. • Phage SA46-CTH2 was characterized by host range, morphology, and genome sequencing. • SA46-CTH2 significantly reduced both planktonic and biofilm cells of S. aureus. • Combination of SA46-CTH2 and nisin inhibited the regrowth of S. aureus.
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Reuter M, Kruger DH. Approaches to optimize therapeutic bacteriophage and bacteriophage-derived products to combat bacterial infections. Virus Genes 2020; 56:136-149. [PMID: 32036540 PMCID: PMC7223754 DOI: 10.1007/s11262-020-01735-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Accepted: 01/18/2020] [Indexed: 12/14/2022]
Abstract
The emerging occurrence of antibiotic-resistant bacterial pathogens leads to a recollection of bacteriophage as antimicrobial therapeutics. This article presents a short overview of the clinical phage application including their use in military medicine and discusses the genotypic and phenotypic properties of a potential "ideal" therapeutic phage. We describe current efforts to engineer phage for their improved usability in pathogen treatment. In addition, phage can be applied for pathogen detection, selective drug delivery, vaccine development, or food and surface decontamination. Instead of viable phage, (engineered) phage-derived enzymes, such as polysaccharide depolymerases or peptidoglycan-degrading enzymes, are considered as promising therapeutic candidates. Finally, we briefly summarize the use of phage for the detection and treatment of "Category A priority pathogens".
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Affiliation(s)
- Monika Reuter
- Institute of Virology, Helmut-Ruska-Haus, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Detlev H. Kruger
- Institute of Virology, Helmut-Ruska-Haus, Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
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48
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Santiago AJ, Burgos-Garay ML, Kartforosh L, Mazher M, Donlan RM. Bacteriophage treatment of carbapenemase-producing Klebsiella pneumoniae in a multispecies biofilm: a potential biocontrol strategy for healthcare facilities. AIMS Microbiol 2020; 6:43-63. [PMID: 32226914 PMCID: PMC7099197 DOI: 10.3934/microbiol.2020003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 02/13/2020] [Indexed: 12/12/2022] Open
Abstract
The p-traps of hospital handwashing sinks represent a potential reservoir for antimicrobial-resistant organisms of major public health concern, such as carbapenemase-producing KPC+ Klebsiella pneumoniae (CPKP). Bacteriophages have reemerged as potential biocontrol agents, particularly against biofilm-associated, drug-resistant microorganisms. The primary objective of our study was to formulate a phage cocktail capable of targeting a CPKP strain (CAV1016) at different stages of colonization within polymicrobial drinking water biofilms using a CDC biofilm reactor (CBR) p-trap model. A cocktail of four CAV1016 phages, all exhibiting depolymerase activity, were isolated from untreated wastewater using standard methods. Biofilms containing Pseudomonas aeruginosa, Micrococcus luteus, Stenotrophomonas maltophilia, Elizabethkingia anophelis, Cupriavidus metallidurans, and Methylobacterium fujisawaense were established in the CBR p-trap model for a period of 28 d. Subsequently, CAV1016 was inoculated into the p-trap model and monitored over a period of 21 d. Biofilms were treated for 2 h at either 25 °C or 37 °C with the phage cocktail (109 PFU/ml) at 7, 14, and 21 d post-inoculation. The effect of phage treatment on the viability of biofilm-associated CAV1016 was determined by plate count on m-Endo LES agar. Biofilm heterotrophic plate counts (HPC) were determined using R2A agar. Phage titers were determined by plaque assay. Phage treatment reduced biofilm-associated CAV1016 viability by 1 log10 CFU/cm2 (p < 0.05) at 7 and 14 d (37 °C) and 1.4 log10 and 1.6 log10 CFU/cm2 (p < 0.05) at 7 and 14 d, respectively (25 °C). No significant reduction was observed at 21 d post-inoculation. Phage treatment had no significant effect on the biofilm HPCs (p > 0.05) at any time point or temperature. Supplementation with a non-ionic surfactant appears to enhance phage association within biofilms. The results of this study suggest the potential of phages to control CPKP and other carbapenemase-producing organisms associated with microbial biofilms in the healthcare environment.
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Affiliation(s)
| | | | | | | | - Rodney M. Donlan
- Clinical and Environmental Microbiology Branch, Division of Healthcare Quality Promotion, Centers for Disease Control and Prevention, Atlanta, GA, USA
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49
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Knecht LE, Veljkovic M, Fieseler L. Diversity and Function of Phage Encoded Depolymerases. Front Microbiol 2020; 10:2949. [PMID: 31998258 PMCID: PMC6966330 DOI: 10.3389/fmicb.2019.02949] [Citation(s) in RCA: 142] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 12/09/2019] [Indexed: 12/14/2022] Open
Abstract
Bacteriophages of the Podoviridae family often exhibit so-called depolymerases as structural components of the virion. These enzymes appear as tail spike proteins (TSPs). After specific binding to capsular polysaccharides (CPS), exopolysaccharides (EPS) or lipopolysaccharide (LPS) of the host bacteria, polysaccharide-repeating units are specifically cleaved. Finally, the phage reaches the last barrier, the cell wall, injects its DNA, and infects the cell. Recently, similar enzymes from bacteriophages of the Ackermannviridae, Myoviridae, and Siphoviridae families were also described. In this mini-review the diversity and function of phage encoded CPS-, EPS-, and LPS-degrading depolymerases is summarized. The function of the enzymes is described in terms of substrate specificity and applications in biotechnology.
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Affiliation(s)
- Leandra E Knecht
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Marjan Veljkovic
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, Wädenswil, Switzerland
| | - Lars Fieseler
- Institute of Food and Beverage Innovation, Zurich University of Applied Sciences, Wädenswil, Switzerland
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50
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Promises and Pitfalls of In Vivo Evolution to Improve Phage Therapy. Viruses 2019; 11:v11121083. [PMID: 31766537 PMCID: PMC6950294 DOI: 10.3390/v11121083] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 11/13/2019] [Accepted: 11/18/2019] [Indexed: 12/26/2022] Open
Abstract
Phage therapy is the use of bacterial viruses (phages) to treat bacterial infections, a medical intervention long abandoned in the West but now experiencing a revival. Currently, therapeutic phages are often chosen based on limited criteria, sometimes merely an ability to plate on the pathogenic bacterium. Better treatment might result from an informed choice of phages. Here we consider whether phages used to treat the bacterial infection in a patient may specifically evolve to improve treatment on that patient or benefit subsequent patients. With mathematical and computational models, we explore in vivo evolution for four phage properties expected to influence therapeutic success: generalized phage growth, phage decay rate, excreted enzymes to degrade protective bacterial layers, and growth on resistant bacteria. Within-host phage evolution is strongly aligned with treatment success for phage decay rate but only partially aligned for phage growth rate and growth on resistant bacteria. Excreted enzymes are mostly not selected for treatment success. Even when evolution and treatment success are aligned, evolution may not be rapid enough to keep pace with bacterial evolution for maximum benefit. An informed use of phages is invariably superior to naive reliance on within-host evolution.
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