1
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Qin K, Shi X, Yang K, Xu Q, Wang F, Chen S, Xu T, Liu J, Wen W, Chen R, Liu Z, Cui L, Zhou K. Phage-antibiotic synergy suppresses resistance emergence of Klebsiella pneumoniae by altering the evolutionary fitness. mBio 2024:e0139324. [PMID: 39248568 DOI: 10.1128/mbio.01393-24] [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: 05/29/2024] [Accepted: 08/13/2024] [Indexed: 09/10/2024] Open
Abstract
Phage-antibiotic synergy (PAS) represents a superior treatment strategy for pathogen infections with less probability of resistance development. Here, we aim to understand the molecular mechanism by which PAS suppresses resistance in terms of population evolution. A novel hypervirulent Klebsiella pneumoniae (KP) phage H5 was genetically and structurally characterized. The combination of H5 and ceftazidime (CAZ) showed a robust synergistic effect in suppressing resistance emergence. Single-cell Raman analysis showed that the phage-CAZ combination suppressed bacterial metabolic activities, contrasting with the upregulation observed with phage alone. The altered population evolutionary trajectory was found to be responsible for the contrasting metabolic activities under different selective pressures, resulting in pleiotropic effects. A pre-existing wcaJ point mutation (wcaJG949A) was exclusively selected by H5, conferring a fitness advantage and up-regulated activity of carbohydrate metabolism, but also causing a trade-off between phage resistance and collateral sensitivity to CAZ. The wcaJ point mutation was counter-selected by H5-CAZ, inducing various mutations in galU that imposed evolutionary disadvantages with higher fitness costs, and suppressed carbohydrate metabolic activity. H5 and H5-CAZ treatments resulted in opposite effects on the transcriptional activity of the phosphotransferase system and the ascorbate and aldarate metabolism pathway, suggesting potential targets for phage resistance suppression. Our study reveals a novel mechanism of resistance suppression by PAS, highlighting how the complexity of bacterial adaptation to selective pressures drives treatment outcomes. IMPORTANCE Phage-antibiotic synergy (PAS) has been recently proposed as a superior strategy for the treatment of multidrug-resistant pathogens to effectively reduce bacterial load and slow down both phage and antibiotic resistance. However, the underlying mechanisms of resistance suppression by PAS have been poorly and rarely been studied. In this study, we tried to understand how PAS suppresses the emergence of resistance using a hypervirulent Klebsiella pneumoniae (KP) strain and a novel phage H5 in combination with ceftazidime (CAZ) as a model. Our study reveals a novel mechanism by which PAS drives altered evolutionary trajectory of bacterial populations, leading to suppressed emergence of resistance. The findings advance our understanding of how PAS suppresses the emergence of resistance, and are imperative for optimizing the efficacy of phage-antibiotic therapy to further improve clinical outcomes.
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Affiliation(s)
- Kunhao Qin
- Department of Pathogen Biology, Shenzhen University Medical School, Shenzhen, China
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
- Jiangxi Province Key Laboratory of Organ Development and Epigenetics, Clinical Medical Research Center, Affiliated Hospital of Jinggangshan University, Health Science Center, Medical Department of Jinggangshan University, Ji'an, China
| | - Xing Shi
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Kai Yang
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Qiuqing Xu
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Fuxing Wang
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen, China
| | - Senxiong Chen
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen, China
| | - Tingting Xu
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Jinquan Liu
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Wangrong Wen
- Clinical Laboratory, The Affiliated Shunde Hospital of Jinan University, Foshan, China
- Clinical Laboratory Centre, The First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Rongchang Chen
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
| | - Zheng Liu
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, Chinese University of Hong Kong, Shenzhen, China
| | - Li Cui
- Key Laboratory of Urban Environment and Health, Fujian Key Laboratory of Watershed Ecology, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Kai Zhou
- Department of Pathogen Biology, Shenzhen University Medical School, Shenzhen, China
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, China
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2
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Santamaría-Corral G, Pagán I, Aguilera-Correa JJ, Esteban J, García-Quintanilla M. A Novel Bacteriophage Infecting Multi-Drug- and Extended-Drug-Resistant Pseudomonas aeruginosa Strains. Antibiotics (Basel) 2024; 13:523. [PMID: 38927189 PMCID: PMC11200629 DOI: 10.3390/antibiotics13060523] [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: 04/11/2024] [Revised: 05/13/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
The prevalence of carbapenem-resistant P. aeruginosa has dramatically increased over the last decade, and antibiotics alone are not enough to eradicate infections caused by this opportunistic pathogen. Phage therapy is a fresh treatment that can be administered under compassionate use, particularly against chronic cases. However, it is necessary to thoroughly characterize the virus before therapeutic application. Our work describes the discovery of the novel sequenced bacteriophage, vB_PaeP-F1Pa, containing an integrase, performs a phylogenetical analysis, describes its stability at a physiological pH and temperature, latent period (40 min), and burst size (394 ± 166 particles per bacterial cell), and demonstrates its ability to infect MDR and XDR P. aeruginosa strains. Moreover, this novel bacteriophage was able to inhibit the growth of bacteria inside preformed biofilms. The present study offers a road map to analyze essential areas for successful phage therapy against MDR and XDR P. aeruginosa infections, and shows that a phage containing an integrase is also able to show good in vitro results, indicating that it is very important to perform a genomic analysis before any clinical use, in order to prevent adverse effects in patients.
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Affiliation(s)
- Guillermo Santamaría-Corral
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (G.S.-C.); (J.J.A.-C.); (M.G.-Q.)
| | - Israel Pagán
- Centro de Biotecnología y Genómica de Plantas UPM-INIA/CSIC and E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28223 Madrid, Spain;
| | - John Jairo Aguilera-Correa
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (G.S.-C.); (J.J.A.-C.); (M.G.-Q.)
- CIBERINFEC-Consorcio Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, 28029 Madrid, Spain
| | - Jaime Esteban
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (G.S.-C.); (J.J.A.-C.); (M.G.-Q.)
- CIBERINFEC-Consorcio Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, 28029 Madrid, Spain
| | - Meritxell García-Quintanilla
- Clinical Microbiology Department, IIS-Fundación Jiménez Díaz, Universidad Autónoma de Madrid, 28040 Madrid, Spain; (G.S.-C.); (J.J.A.-C.); (M.G.-Q.)
- CIBERINFEC-Consorcio Centro de Investigación Biomédica en Red (CIBER) de Enfermedades Infecciosas, 28029 Madrid, Spain
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Kallies R, Hu D, Abdulkadir N, Schloter M, Rocha U. Identification of Huge Phages from Wastewater Metagenomes. Viruses 2023; 15:2330. [PMID: 38140571 PMCID: PMC10747093 DOI: 10.3390/v15122330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 11/20/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023] Open
Abstract
Huge phages have genomes larger than 200 kilobases, which are particularly interesting for their genetic inventory and evolution. We screened 165 wastewater metagenomes for the presence of viral sequences. After identifying over 600 potential huge phage genomes, we reduced the dataset using manual curation by excluding viral contigs that did not contain viral protein-coding genes or consisted of concatemers of several small phage genomes. This dataset showed seven fully annotated huge phage genomes. The phages grouped into distinct phylogenetic clades, likely forming new genera and families. A phylogenomic analysis between our huge phages and phages with smaller genomes, i.e., less than 200 kb, supported the hypothesis that huge phages have undergone convergent evolution. The genomes contained typical phage protein-coding genes, sequential gene cassettes for metabolic pathways, and complete inventories of tRNA genes covering all standard and rare amino acids. Our study showed a pipeline for huge phage analyses that may lead to new enzymes for therapeutic or biotechnological applications.
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Affiliation(s)
- René Kallies
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Die Hu
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Nafi’u Abdulkadir
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
| | - Michael Schloter
- Department of Environmental Health, Helmholtz Munich, Ingolstaedter Landstr. 1, D-85758 Neuherberg, Germany;
| | - Ulisses Rocha
- Department for Environmental Microbiology, Helmholtz Centre for Environmental Research, Permoserstr. 15, D-04318 Leipzig, Germany; (D.H.); (N.A.)
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4
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Zhao X, Sun C, Jin M, Chen J, Xing L, Yan J, Wang H, Liu Z, Chen WH. Enrichment Culture but Not Metagenomic Sequencing Identified a Highly Prevalent Phage Infecting Lactiplantibacillus plantarum in Human Feces. Microbiol Spectr 2023; 11:e0434022. [PMID: 36995238 PMCID: PMC10269749 DOI: 10.1128/spectrum.04340-22] [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: 10/27/2022] [Accepted: 03/07/2023] [Indexed: 03/31/2023] Open
Abstract
Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human diseases, but its phages in the human gut remain unexplored. Here, we report its first gut phage, Gut-P1, which we systematically screened using metagenomic sequencing, virus-like particle (VLP) sequencing, and enrichment culture from 35 fecal samples. Gut-P1 is virulent, belongs to the Douglaswolinvirus genus, and is highly prevalent in the gut (~11% prevalence); it has a genome of 79,928 bp consisting of 125 protein coding genes and displaying low sequence similarities to public L. plantarum phages. Physiochemical characterization shows that it has a short latent period and adapts to broad ranges of temperatures and pHs. Furthermore, Gut-P1 strongly inhibits the growth of L. plantarum strains at a multiplicity of infection (MOI) of 1e-6. Together, these results indicate that Gut-P1 can greatly impede the application of L. plantarum in humans. Strikingly, Gut-P1 was identified only in the enrichment culture, not in our metagenomic or VLP sequencing data nor in any public human phage databases, indicating the inefficiency of bulk sequencing in recovering low-abundance but highly prevalent phages and pointing to the unexplored hidden diversity of the human gut virome despite recent large-scale sequencing and bioinformatics efforts. IMPORTANCE As Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human gut-related diseases, its bacteriophages may pose a certain threat to their further application and should be identified and characterized more often from the human intestine. Here, we isolated and identified the first gut L. plantarum phage that is prevalent in a Chinese population. This phage, Gut-P1, is virulent and can strongly inhibit the growth of multiple L. plantarum strains at low MOIs. Our results also show that bulk sequencing is inefficient at recovering low-abundance but highly prevalent phages such as Gut-P1, suggesting that the hidden diversity of human enteroviruses has not yet been explored. Our results call for innovative approaches to isolate and identify intestinal phages from the human gut and to rethink our current understanding of the enterovirus, particularly its underestimated diversity and overestimated individual specificity.
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Affiliation(s)
- Xueyang Zhao
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Chuqing Sun
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Menglu Jin
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jingchao Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Lulu Xing
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Jin Yan
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Hailei Wang
- College of Life Science, Henan Normal University, Xinxiang, Henan, China
| | - Zhi Liu
- Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
| | - Wei-Hua Chen
- Key Laboratory of Molecular Biophysics of the Ministry of Education, Hubei Key Laboratory of Bioinformatics and Molecular-imaging, Center for Artificial Intelligence Biology, Department of Bioinformatics and Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
- Institution of Medical Artificial Intelligence, Binzhou Medical University, Yantai, China
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5
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Egido JE, Toner-Bartelds C, Costa AR, Brouns SJJ, Rooijakkers SHM, Bardoel BW, Haas PJ. Monitoring phage-induced lysis of gram-negatives in real time using a fluorescent DNA dye. Sci Rep 2023; 13:856. [PMID: 36646746 PMCID: PMC9842612 DOI: 10.1038/s41598-023-27734-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 01/06/2023] [Indexed: 01/18/2023] Open
Abstract
Bacteriophages (phages) are viruses that specifically attack bacteria. Their use as therapeutics, which constitutes a promising alternative to antibiotics, heavily relies on selecting effective lytic phages against the pathogen of interest. Current selection techniques are laborious and do not allow for direct visualization of phage infection dynamics. Here, we present a method that circumvents these limitations. It can be scaled for high-throughput and permits monitoring of the phage infection in real time via a fluorescence signal readout. This is achieved through the use of a membrane-impermeant nucleic acid dye that stains the DNA of damaged or lysed bacteria and new phage progeny. We have tested the method on Pseudomonas aeruginosa and Klebsiella pneumoniae and show that an increase in fluorescence reflects phage-mediated killing. This is confirmed by other techniques including spot tests, colony plating, flow cytometry and metabolic activity measurements. Furthermore, we illustrate how our method may be used to compare the activity of different phages and to screen the susceptibility of clinical isolates to phage. Altogether, we present a fast, reliable way of selecting phages against Gram-negative bacteria, which may be valuable in optimizing the process of selecting phages for therapeutic use.
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Affiliation(s)
- Julia E Egido
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Catherine Toner-Bartelds
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Ana Rita Costa
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
- Kavli Institute of Nanoscience, Delft, The Netherlands
- Fagenbank, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Delft University of Technology, Delft, The Netherlands
- Kavli Institute of Nanoscience, Delft, The Netherlands
- Fagenbank, Delft, The Netherlands
| | - Suzan H M Rooijakkers
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Bart W Bardoel
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands
| | - Pieter-Jan Haas
- Medical Microbiology, University Medical Center Utrecht, Utrecht University, Utrecht, The Netherlands.
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6
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Wannasrichan W, Htoo HH, Suwansaeng R, Pogliano J, Nonejuie P, Chaikeeratisak V. Phage-resistant Pseudomonas aeruginosa against a novel lytic phage JJ01 exhibits hypersensitivity to colistin and reduces biofilm production. Front Microbiol 2022; 13:1004733. [PMID: 36274728 PMCID: PMC9583000 DOI: 10.3389/fmicb.2022.1004733] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Pseudomonas aeruginosa, a major cause of nosocomial infections, has been categorized by World Health Organization as a critical pathogen urgently in need of effective therapies. Bacteriophages or phages, which are viruses that specifically kill bacteria, have been considered as alternative agents for the treatment of bacterial infections. Here, we discovered a lytic phage targeting P. aeruginosa, designated as JJ01, which was classified as a member of the Myoviridae family due to the presence of an icosahedral capsid and a contractile tail under TEM. Phage JJ01 requires at least 10 min for 90% of its particles to be adsorbed to the host cells and has a latent period of 30 min inside the host cell for its replication. JJ01 has a relatively large burst size, which releases approximately 109 particles/cell at the end of its lytic life cycle. The phage can withstand a wide range of pH values (3–10) and temperatures (4–60°C). Genome analysis showed that JJ01 possesses a complete genome of 66,346 base pairs with 55.7% of GC content, phylogenetically belonging to the genus Pbunavirus. Genome annotation further revealed that the genome encodes 92 open reading frames (ORFs) with 38 functionally predictable genes, and it contains neither tRNA nor toxin genes, such as drug-resistant or lysogenic-associated genes. Phage JJ01 is highly effective in suppressing bacterial cell growth for 12 h and eradicating biofilms established by the bacteria. Even though JJ01-resistant bacteria have emerged, the ability of phage resistance comes with the expense of the bacterial fitness cost. Some resistant strains were found to produce less biofilm and grow slower than the wild-type strain. Among the resistant isolates, the resistant strain W10 which notably loses its physiological fitness becomes eight times more susceptible to colistin and has its cell membrane compromised, compared to the wild type. Altogether, our data revealed the potential of phage JJ01 as a candidate for phage therapy against P. aeruginosa and further supports that even though the use of phages would subsequently lead to the emergence of phage-resistant bacteria, an evolutionary trade-off would make them more sensitive to antibiotics.
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Affiliation(s)
- Wichanan Wannasrichan
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Htut Htut Htoo
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Rubsadej Suwansaeng
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- *Correspondence: Vorrapon Chaikeeratisak,
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7
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Landa KJ, Mossman LM, Whitaker RJ, Rapti Z, Clifton SM. Phage-Antibiotic Synergy Inhibited by Temperate and Chronic Virus Competition. Bull Math Biol 2022; 84:54. [PMID: 35316421 DOI: 10.1007/s11538-022-01006-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022]
Abstract
As antibiotic resistance grows more frequent for common bacterial infections, alternative treatment strategies such as phage therapy have become more widely studied in the medical field. While many studies have explored the efficacy of antibiotics, phage therapy, or synergistic combinations of phages and antibiotics, the impact of virus competition on the efficacy of antibiotic treatment has not yet been considered. Here, we model the synergy between antibiotics and two viral types, temperate and chronic, in controlling bacterial infections. We demonstrate that while combinations of antibiotic and temperate viruses exhibit synergy, competition between temperate and chronic viruses inhibits bacterial control with antibiotics. In fact, our model reveals that antibiotic treatment may counterintuitively increase the bacterial load when a large fraction of the bacteria are antibiotic resistant, and both chronic and temperate phages are present.
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Affiliation(s)
- Kylie J Landa
- Department of Mathematics, Statistics, and Computer Science, St. Olaf College, Northfield, MN, 55057, USA
| | - Lauren M Mossman
- Department of Mathematics, Statistics, and Computer Science, St. Olaf College, Northfield, MN, 55057, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zoi Rapti
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Mathematics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sara M Clifton
- Department of Mathematics, Statistics, and Computer Science, St. Olaf College, Northfield, MN, 55057, USA.
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8
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Kazantseva OA, Buzikov RM, Pilipchuk TA, Valentovich LN, Kazantsev AN, Kalamiyets EI, Shadrin AM. The Bacteriophage Pf-10-A Component of the Biopesticide "Multiphage" Used to Control Agricultural Crop Diseases Caused by Pseudomonas syringae. Viruses 2021; 14:42. [PMID: 35062246 PMCID: PMC8779105 DOI: 10.3390/v14010042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/16/2022] Open
Abstract
Phytopathogenic pseudomonads are widespread in the world and cause a wide range of plant diseases. In this work, we describe the Pseudomonas phage Pf-10, which is a part of the biopesticide "Multiphage" used for bacterial diseases of agricultural crops caused by Pseudomonas syringae. The Pf-10 chromosome is a dsDNA molecule with two direct terminal repeats (DTRs). The phage genomic DNA is 39,424 bp long with a GC-content of 56.5%. The Pf-10 phage uses a packaging mechanism based on T7-like short DTRs, and the length of each terminal repeat is 257 bp. Electron microscopic analysis has shown that phage Pf-10 has the podovirus morphotype. Phage Pf-10 is highly stable at pH values from 5 to 10 and temperatures from 4 to 60 °C and has a lytic activity against Pseudomonas strains. Phage Pf-10 is characterized by fast adsorption rate (80% of virions attach to the host cells in 10 min), but has a relatively small number of progeny (37 ± 8.5 phage particles per infected cell). According to the phylogenetic analysis, phage Pf-10 can be classified as a new phage species belonging to the genus Pifdecavirus, subfamily Studiervirinae, family Autographiviridae, order Caudovirales.
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Affiliation(s)
- Olesya A. Kazantseva
- Laboratory of Bacteriophage Biology, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290 Pushchino, Russia;
| | - Rustam M. Buzikov
- Laboratory of Bacteriophage Biology, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290 Pushchino, Russia;
| | - Tatsiana A. Pilipchuk
- Institute of Microbiology, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.A.P.); (L.N.V.); (E.I.K.)
| | - Leonid N. Valentovich
- Institute of Microbiology, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.A.P.); (L.N.V.); (E.I.K.)
- Faculty of Biology, Belarusian State University, 220030 Minsk, Belarus
| | - Andrey N. Kazantsev
- P. N. Lebedev Physical Institute of the Russian Academy of Sciences, Pushchino Radio Astronomy Observatory, 142290 Pushchino, Russia;
| | - Emilia I. Kalamiyets
- Institute of Microbiology, The National Academy of Sciences of Belarus, 220141 Minsk, Belarus; (T.A.P.); (L.N.V.); (E.I.K.)
| | - Andrey M. Shadrin
- Laboratory of Bacteriophage Biology, G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms, Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Federal Research Center, 142290 Pushchino, Russia;
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9
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Xu J, Zhang R, Yu X, Zhang X, Liu G, Liu X. Molecular Characteristics of Novel Phage vB_ShiP-A7 Infecting Multidrug-Resistant Shigella flexneri and Escherichia coli, and Its Bactericidal Effect in vitro and in vivo. Front Microbiol 2021; 12:698962. [PMID: 34512574 PMCID: PMC8427288 DOI: 10.3389/fmicb.2021.698962] [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: 04/22/2021] [Accepted: 07/19/2021] [Indexed: 01/21/2023] Open
Abstract
In recent years, increasing evidence has shown that bacteriophages (phages) can inhibit infection caused by multidrug-resistant (MDR) bacteria. Here, we isolated a new phage, named vB_ShiP-A7, using MDR Shigella flexneri as the host. vB_ShiP-A7 is a novel member of Podoviridae, with a latency period of approximately 35 min and a burst size of approximately 100 phage particles/cell. The adsorption rate constant of phage vB_ShiP-A7 to its host S. flexneri was 1.405 × 10–8 mL/min. The vB_ShiP-A7 genome is a linear double-stranded DNA composed of 40,058 bp with 177 bp terminal repeats, encoding 43 putative open reading frames. Comparative genomic analysis demonstrated that the genome sequence of vB_ShiP-A7 is closely related to 15 different phages, which can infect different strains. Mass spectrometry analysis revealed that 12 known proteins and 6 hypothetical proteins exist in the particles of phage vB_ShiP-A7. Our results confirmed that the genome of vB_ShiP-A7 is free of lysogen-related genes, bacterial virulence genes, and antibiotic resistance genes. vB_ShiP-A7 can significantly disrupt the growth of some MDR clinical strains of S. flexneri and Escherichia coli in liquid culture and biofilms in vitro. In addition, vB_ShiP-A7 can reduce the load of S. flexneri by approximately 3–10 folds in an infection model of mice. Therefore, vB_ShiP-A7 is a stable novel phage with the potential to treat infections caused by MDR strains of S. flexneri and E. coli.
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Affiliation(s)
- Jing Xu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, China.,Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Ruiyang Zhang
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, China.,Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Xinyan Yu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, China.,Department of Microbiology, Nanjing Medical University, Nanjing, China
| | - Xuesen Zhang
- State Key Laboratory of Reproductive Medicine, Nanjing Medical University, Nanjing, China
| | - Genyan Liu
- Department of Laboratory Medicine, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China.,National Key Clinical Department of Laboratory Medicine, The First Affiliated Hospital With Nanjing Medical University, Nanjing, China
| | - Xiaoqiu Liu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Nanjing Medical University, Nanjing, China.,Department of Microbiology, Nanjing Medical University, Nanjing, China
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10
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Han P, Hu Y, An X, Song L, Fan H, Tong Y. Biochemical and genomic characterization of a novel bacteriophage BUCT555 lysing Stenotrophomonas maltophilia. Virus Res 2021; 301:198465. [PMID: 34052250 DOI: 10.1016/j.virusres.2021.198465] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 05/20/2021] [Accepted: 05/21/2021] [Indexed: 12/25/2022]
Abstract
Stenotrophomonas maltophilia is a common conditional pathogen, and it is naturally resistant to most commonly used clinical antibiotics. The bacteriophage is considered to be a potential antibiotic alternative for treating multi-drug-resistant bacteria. In this study, a bacteriophage BUCT555 was isolated from hospital sewage for lysing the clinical multi-drug resistant Stenotrophomonas maltophilia. Electron microscopy studies revealed this phage belongs to the Podoviridae family. The double-stranded DNA genome of bacteriophage BUCT555 is composed of 39,440 bp with a GC content of 61.43%. The genome contains 57 open reading frames, 14 of which had assigned functions, while no virulence related genes, antibiotic resistance genes or tRNA were identified. The burst size of BUCT555 was 204 pfu per infected cell. Structure proteins of bacteriophage BUCT555 generated by SDS-PAGE and HPLC-MS revealed that it contains seven proteins with molecular weight ranging from 19 to 89 kDa. BLASTn analysis showed that phage BUCT555 has 2% homology with other phages in NCBI database, suggesting BUCT555 is a new phage genus of Podoviridae that infects Stenotrophomonas maltophilia. Characterization of the bacteriophage BUCT555 enriches our knowledge about the diversity of Stenotrophomonas maltophilia bacteriophages.
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Affiliation(s)
- Pengjun Han
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yunjia Hu
- 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
| | - Lihua Song
- 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.
| | - 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, Beijing University of Chemical Technology, Beijing 100029, China.
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11
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Temperate and chronic virus competition leads to low lysogen frequency. J Theor Biol 2021; 523:110710. [PMID: 33839160 DOI: 10.1016/j.jtbi.2021.110710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 11/23/2022]
Abstract
The canonical bacteriophage is obligately lytic: the virus infects a bacterium and hijacks cell functions to produce large numbers of new viruses which burst from the cell. These viruses are well-studied, but there exist a wide range of coexisting virus lifestyles that are less understood. Temperate viruses exhibit both a lytic cycle and a latent (lysogenic) cycle, in which viral genomes are integrated into the bacterial host. Meanwhile, chronic (persistent) viruses use cell functions to produce more viruses without killing the cell; chronic viruses may also exhibit a latent stage in addition to the productive stage. Here, we study the ecology of these competing viral strategies. We demonstrate the conditions under which each strategy is dominant, which aids in control of human bacterial infections using viruses. We find that low lysogen frequencies provide competitive advantages for both virus types; however, chronic viruses maximize steady state density by eliminating lysogeny entirely, while temperate viruses exhibit a non-zero 'sweet spot' lysogen frequency. Viral steady state density maximization leads to coexistence of temperate and chronic viruses, explaining the presence of multiple viral strategies in natural environments.
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12
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Abstract
With the fast emergence of serious antibiotic resistance and the lagged discovery of novel antibacterial drugs, phage therapy for pathogenic bacterial infections has acquired great attention in the clinics. However, development of therapeutic phages also faces tough challenges, such as laborious screening and time to generate effective phage drugs since each phage may only lyse a narrow scope of bacterial strains. Identifying highly effective phages with broad host ranges is crucial for improving phage therapy. Here, we isolated and characterized several lytic phages from various environments specific for Pseudomonas aeruginosa by testing their growth, invasion, host ranges, and potential for killing targeted bacteria. Importantly, we identified several therapeutic phages (HX1, PPY9, and TH15) with broad host ranges to lyse laboratory strains and clinical isolates of P. aeruginosa with multi-drug resistance (MDR) both in vitro and in mouse models. In addition, we analyzed critical genetic traits related to the high-level broad host coverages by genome sequencing and subsequent computational analysis against known phages. Collectively, our findings establish that these novel phages may have potential for further development as therapeutic options for patients who fail to respond to conventional treatments.IMPORTANCE Novel lytic phages isolated from various environmental settings were systematically characterized for their critical genetic traits, morphology structures, host ranges against laboratory strains and clinical multi-drug resistant (MDR) Pseudomonas aeruginosa, and antibacterial capacity both in vitro and in mouse models. First, we characterized the genetic traits and compared with other existing phages. Furthermore, we utilized acute pneumonia induced by laboratorial strain PAO1, and W19, an MDR clinical isolate and chronic pneumonia by agar beads laden with FDR1, a mucoid phenotype strain isolated from the sputum of a cystic fibrosis (CF) patient. Consequently, we found that these phages not only suppress bacteria in vitro but also significantly reduce the infection symptom and disease progression in vivo, including lowered bug burdens, inflammatory responses and lung injury in mice, suggesting that they may be further developed as therapeutic agents against MDR P. aeruginosa.
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Shi X, Zhao F, Sun H, Yu X, Zhang C, Liu W, Pan Q, Ren H. Characterization and Complete Genome Analysis of Pseudomonas aeruginosa Bacteriophage vB_PaeP_LP14 Belonging to Genus Litunavirus. Curr Microbiol 2020; 77:2465-2474. [PMID: 32367280 DOI: 10.1007/s00284-020-02011-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/24/2020] [Indexed: 12/17/2022]
Abstract
A lytic Pseudomonas aeruginosa phage vB_PaeP_LP14 belonging to the family Podoviridae was isolated from infected mink. The microbiological characterization revealed that LP14 was stable at 40 to 50 °C and stable over a broad range of pH (5 to 12). The latent period was 5 min, and the burst size was 785 pfu/infected cell. The whole-genome sequencing showed that LP14 was a dsDNA virus and has a genome of 73,080 bp. The genome contained 93 predicted open reading frames (ORFs), 17 of which have known functions including DNA replication and modification, transcriptional regulation, structural and packaging proteins, and host cell lysis. No tRNA genes were identified. BLASTn analysis revealed that phage LP14 had a high-sequence identity (96%) with P. aeruginosa phage YH6. Both morphological characterization and genome annotation indicate that phage LP14 is a memberof the family Podoviridae genus Litunavirus. The study of phage LP14 will provide basic information for further research on treatment of P. aeruginosa infections.
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Affiliation(s)
- Xiaojie Shi
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Feiyang Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Huzhi Sun
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Xiaoyan Yu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China.
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14
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Abstract
Antibiotic resistance is a growing concern for management of common bacterial infections. Here, we show that antibiotics can be effective at subinhibitory levels when bacteria carry latent phage. Our findings suggest that specific treatment strategies based on the identification of latent viruses in individual bacterial strains may be an effective personalized medicine approach to antibiotic stewardship. Most bacteria and archaea are infected by latent viruses that change their physiology and responses to environmental stress. We use a population model of the bacterium-phage relationship to examine the role that latent phage play in the bacterial population over time in response to antibiotic treatment. We demonstrate that the stress induced by antibiotic administration, even if bacteria are resistant to killing by antibiotics, is sufficient to control the infection under certain conditions. This work expands the breadth of understanding of phage-antibiotic synergy to include both temperate and chronic viruses persisting in their latent form in bacterial populations. IMPORTANCE Antibiotic resistance is a growing concern for management of common bacterial infections. Here, we show that antibiotics can be effective at subinhibitory levels when bacteria carry latent phage. Our findings suggest that specific treatment strategies based on the identification of latent viruses in individual bacterial strains may be an effective personalized medicine approach to antibiotic stewardship.
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Identification of novel bacteriophage vB_EcoP-EG1 with lytic activity against planktonic and biofilm forms of uropathogenic Escherichia coli. Appl Microbiol Biotechnol 2018; 103:315-326. [PMID: 30397766 DOI: 10.1007/s00253-018-9471-x] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 12/28/2022]
Abstract
Urinary tract infections are one of the most common infectious diseases worldwide. Uropathogenic Escherichia coli (UPEC) is a major cause of unary tract infection. Due to increasing prevalence of multidrug resistance, alternative methods to eradicate the UPECs are urgently needed. In this respect, phage therapy has been demonstrated to be a good candidate. Here, we described a novel bacteriophage named vB_EcoP-EG1, which can infect several strains of UPEC. Phage morphology and genome sequencing analysis show that vB_EcoP-EG1 belongs to the T7-like Podoviridae. vB_EcoP-EG1 possesses a genome (39,919 bp) containing 51 predicted genes and 149 bp terminal repeats. vB_EcoP-EG1 genome does not encode toxic proteins or proteins related to lysogeny. And no known virulent proteins were found in purified phage particles by mass spectrometry. vB_EcoP-EG1 appeared to be relatively specific and sensitive to clinical UPEC strains, which could infect 10 out of 21 clinical multidrug-resistant UPEC strains. In addition, vB_EcoP-EG1 suspension can eliminate biofilm formed by E. coli MG1655 and multidrug-resistant UPEC strain 390G7. Therefore, we concluded that vB_EcoP-EG1 has desirable characteristics for potential therapy, which may serve as an alternative to antibiotic therapy against urinary tract infections caused by multidrug-resistant UPEC.
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da Silva Xavier A, da Silva FP, Vidigal PMP, Lima TTM, de Souza FO, Alfenas-Zerbini P. Genomic and biological characterization of a new member of the genus Phikmvvirus infecting phytopathogenic Ralstonia bacteria. Arch Virol 2018; 163:3275-3290. [DOI: 10.1007/s00705-018-4006-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 08/10/2018] [Indexed: 02/07/2023]
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