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Lossouarn J, Beurrier E, Bouteau A, Moncaut E, Sir Silmane M, Portalier H, Zouari A, Cattoir V, Serror P, Petit MA. The virtue of training: extending phage host spectra against vancomycin-resistant Enterococcus faecium strains using the Appelmans method. Antimicrob Agents Chemother 2024; 68:e0143923. [PMID: 38591854 DOI: 10.1128/aac.01439-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 03/14/2024] [Indexed: 04/10/2024] Open
Abstract
Phage therapy has (re)emerged as a serious possibility for combating multidrug-resistant bacterial infections, including those caused by vancomycin-resistant Enterococcus faecium strains. These opportunistic pathogens belong to a specific clonal complex 17, against which relatively few phages have been screened. We isolated a collection of 21 virulent phages growing on these vancomycin-resistant isolates. Each of these phages harbored a typical narrow plaquing host range, lysing at most 5 strains and covering together 10 strains of our panel of 14 clinical isolates. To enlarge the host spectrum of our phages, the Appelmans protocol was used. We mixed four out of our most complementary phages in a cocktail that we iteratively grew on eight naive strains from our panel, of which six were initially refractory to at least three of the combined phages. Fifteen successive passages permitted to significantly improve the lytic activity of the cocktail, from which phages with extended host ranges within the E. faecium species could be isolated. A single evolved phage able to kill up to 10 of the 14 initial E. faecium strains was obtained, and it barely infected nearby species. All evolved phages had acquired point mutations or a recombination event in the tail fiber genetic region, suggesting these genes might have driven phage evolution by contributing to their extended host spectra.
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Affiliation(s)
- Julien Lossouarn
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Elsa Beurrier
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Astrid Bouteau
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Elisabeth Moncaut
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Maria Sir Silmane
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Heïdi Portalier
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Asma Zouari
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière et CNR de la Résistance aux Antibiotiques (laboratoire associé "Entérocoques"), Rennes, France
| | - Vincent Cattoir
- CHU de Rennes, Service de Bactériologie-Hygiène Hospitalière et CNR de la Résistance aux Antibiotiques (laboratoire associé "Entérocoques"), Rennes, France
- Université de Rennes, INSERM, UMR_S1230 BRM, Rennes, France
| | - Pascale Serror
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Marie-Agnès Petit
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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2
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Tadeu AD, Duarte J, Trindade D, Costa P, Venâncio C, Lopes I, Oliveira V, Gomes NCM, Almeida A, Pereira C. Bacteriophages to control Vibrio alginolyticus in live feeds prior to their administration in larviculture. J Appl Microbiol 2024; 135:lxae115. [PMID: 38710582 DOI: 10.1093/jambio/lxae115] [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: 02/20/2024] [Revised: 04/16/2024] [Accepted: 05/04/2024] [Indexed: 05/08/2024]
Abstract
AIMS This study aimed to evaluate the efficiency of two phages [VB_VaC_TDDLMA (phage TDD) and VB_VaC_SRILMA (phage SRI)] alone and in a cocktail to control Vibrio alginolyticus in brine shrimp before their administration in larviculture. METHODS AND RESULTS Phages were isolated from seawater samples and characterized by host spectrum, growth parameters, adsorption rate, genomic analysis, and inactivation efficiency. Both phages belong to the Caudoviricetes class and lack known virulence or antibiotic-resistance genes. They exhibit specificity, infecting only their host, V. alginolyticus CECT 521. Preliminary experiments in a culture medium showed that phage TDD (reduction of 5.8 log CFU ml-1 after 10 h) outperformed phage SRI (reduction of 4.6 log CFU ml-1 after 6 h) and the cocktail TDD/SRI (reduction of 5.2 log CFU ml-1 after 8 h). In artificial marine water experiments with Artemia franciscana, both single phage suspensions and the phage cocktail, effectively inactivated V. alginolyticus in culture water (reduction of 4.3, 2.1, and 1.9 log CFU ml-1 for phages TDD, SRI, and the phage cocktail, respectively, after 12 h) and in A. franciscana (reduction of 51.6%, 87.3%, and 85.3% for phages TDD, SRI, and the phage cocktail, respectively, after 24 h). The two phages and the phage cocktail did not affect A. franciscana natural microbiota or other Vibrio species in the brine shrimp. CONCLUSIONS The results suggest that phages can safely and effectively control V. alginolyticus in A. franciscana prior to its administration in larviculture.
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Affiliation(s)
- Amanda Dias Tadeu
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - João Duarte
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - David Trindade
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Pedro Costa
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Cátia Venâncio
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Isabel Lopes
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Vanessa Oliveira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Newton C M Gomes
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Adelaide Almeida
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
| | - Carla Pereira
- Department of Biology and CESAM, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
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3
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Vaz CSL, da Fonseca FN, Voss-Rech D, Morés MAZ, Coldebella A, Cantão ME. Wild-type lytic bacteriophages against Salmonella Heidelberg: Further characterization and effect of prophylactic therapy in broiler chickens. Res Vet Sci 2024; 171:105247. [PMID: 38554611 DOI: 10.1016/j.rvsc.2024.105247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 03/22/2024] [Accepted: 03/24/2024] [Indexed: 04/02/2024]
Abstract
To characterize wild-type bacteriophages and their effect on Salmonella Heidelberg intestinal colonization in broilers, phages combined in a cocktail were continuously delivered via drinking water since the first day after hatching. After challenge with a field strain, broilers were evaluated at regular intervals for S. Heidelberg and bacteriophages in tissues and cecum, and gross and microscopic lesions in organs. Phages were highly virulent against S. Heidelberg by efficiency of plating. One-step growth curves exhibited eclipse period from 20 to 25 min, whereas the lowest latent period and higher burst size found were 45 min and 54 PFU/cell, respectively. Bacteriophage whole genomic sequencing analyses revealed a lack of genes related to lysogeny, antimicrobial resistance, and virulence factors. Relevant gross or microscopic lesions were absent in tissues analyzed from treated broilers. Although numerically stable bacteriophage concentrations were detected in the cecal contents of treated broilers, no significant difference was found for the S. Heidelberg cecal load in comparison to the untreated group and for the prevalence of positive tissues throughout the evaluated period. The phages produced turbid plaques against some S. Heidelberg re-isolated from treated broilers, suggesting the evolving of a resistant subpopulation. Overall, the results provide new evidence of the safety and in vitro replication of such phages in S. Heidelberg. Nevertheless, continuous administration of the phage suspension most likely induced the development of bacteriophage-resistant mutants, which might have affected the in vivo effect. Therefore, a putative administration protocol should be based on other strategies, such as short-term therapy at pre-harvest age.
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Affiliation(s)
| | | | - Daiane Voss-Rech
- Embrapa Suínos e Aves, BR 153, Km 110, PO box 321, Concórdia, Santa Catarina 89715899, Brazil
| | | | - Arlei Coldebella
- Embrapa Suínos e Aves, BR 153, Km 110, PO box 321, Concórdia, Santa Catarina 89715899, Brazil
| | - Maurício Egídio Cantão
- Embrapa Suínos e Aves, BR 153, Km 110, PO box 321, Concórdia, Santa Catarina 89715899, Brazil
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4
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Holtappels D, Abelson SA, Nouth SC, Rickus GEJ, Amare SZ, Giller JP, Jian DZ, Koskella B. Genomic characterization of Pseudomonas syringae pv. syringae from Callery pear and the efficiency of associated phages in disease protection. Microbiol Spectr 2024; 12:e0283323. [PMID: 38323825 PMCID: PMC10913373 DOI: 10.1128/spectrum.02833-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 12/11/2023] [Indexed: 02/08/2024] Open
Abstract
The Pseudomonas syringae species complex is a heterogeneous group of plant pathogenic bacteria associated with a wide distribution of plant species. Advances in genomics are revealing the complex evolutionary history of this species complex and the wide array of genetic adaptations underpinning their diverse lifestyles. Here, we genomically characterize two P. syringae isolates collected from diseased Callery pears (Pyrus calleryana) in Berkeley, California in 2019 and 2022. We also isolated a lytic bacteriophage, which we characterized and evaluated for biocontrol efficiency. Using a multilocus sequence analysis and core genome alignment, we classified the P. syringae isolates as members of phylogroup 2, related to other strains previously isolated from Pyrus and Prunus. An analysis of effector proteins demonstrated an evolutionary conservation of effectoromes across isolates classified in PG2 and yet uncovered unique effector profiles for each, including the two newly identified isolates. Whole-genome sequencing of the associated phage uncovered a novel phage genus related to Pseudomonas syringae pv. actinidiae phage PHB09 and the Flaumdravirus genus. Finally, using in planta infection assays, we demonstrate that the phage was equally useful in symptom mitigation of immature pear fruit regardless of the Pss strain tested. Overall, this study demonstrates the diversity of P. syringae and their viruses associated with ornamental pear trees, posing spill-over risks to commercial pear trees and the possibility of using phages as biocontrol agents to reduce the impact of disease.IMPORTANCEGlobal change exacerbates the spread and impact of pathogens, especially in agricultural settings. There is a clear need to better monitor the spread and diversity of plant pathogens, including in potential spillover hosts, and for the development of novel and sustainable control strategies. In this study, we characterize the first described strains of Pseudomonas syringae pv. syringae isolated from Callery pear in Berkeley, California from diseased tissues in an urban environment. We show that these strains have divergent virulence profiles from previously described strains and that they can cause disease in commercial pears. Additionally, we describe a novel bacteriophage that is associated with these strains and explore its potential to act as a biocontrol agent. Together, the data presented here demonstrate that ornamental pear trees harbor novel P. syringae pv. syringae isolates that potentially pose a risk to local fruit production, or vice versa-but also provide us with novel associated phages, effective in disease mitigation.
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Affiliation(s)
- D. Holtappels
- Integrative Biology University of California, Berkeley, California, USA
| | - S. A. Abelson
- Integrative Biology University of California, Berkeley, California, USA
| | - S. C. Nouth
- Integrative Biology University of California, Berkeley, California, USA
| | - G. E. J. Rickus
- Integrative Biology University of California, Berkeley, California, USA
| | - S. Z. Amare
- Integrative Biology University of California, Berkeley, California, USA
| | - J. P. Giller
- Integrative Biology University of California, Berkeley, California, USA
| | - D. Z. Jian
- Integrative Biology University of California, Berkeley, California, USA
| | - B. Koskella
- Integrative Biology University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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5
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Barcia-Cruz R, Goudenège D, Moura de Sousa JA, Piel D, Marbouty M, Rocha EPC, Le Roux F. Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages. Nat Commun 2024; 15:664. [PMID: 38253718 PMCID: PMC10803314 DOI: 10.1038/s41467-024-44965-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/10/2024] [Indexed: 01/24/2024] Open
Abstract
Phage satellites are bacterial genetic elements that co-opt phage machinery for their own dissemination. Here we identify a family of satellites, named Phage-Inducible Chromosomal Minimalist Islands (PICMIs), that are broadly distributed in marine bacteria of the family Vibrionaceae. A typical PICMI is characterized by reduced gene content, does not encode genes for capsid remodelling, and packages its DNA as a concatemer. PICMIs integrate in the bacterial host genome next to the fis regulator, and encode three core proteins necessary for excision and replication. PICMIs are dependent on virulent phage particles to spread to other bacteria, and protect their hosts from other competitive phages without interfering with their helper phage. Thus, our work broadens our understanding of phage satellites and narrows down the minimal number of functions necessary to hijack a tailed phage.
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Affiliation(s)
- Rubén Barcia-Cruz
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - David Goudenège
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France
| | - Jorge A Moura de Sousa
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Damien Piel
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France
| | - Martial Marbouty
- Institut Pasteur, Université Paris Cité, Organization and Dynamics of Viral Genomes Group, CNRS UMR 3525, Paris, F-75015, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Frédérique Le Roux
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff cedex, France.
- Ifremer, Unité Physiologie Fonctionnelle des Organismes Marins, ZI de la Pointe du Diable, CS 10070, F-29280, Plouzané, France.
- Département de microbiologie, infectiologie et immunologie, Université de Montréal, Montréal, Canada.
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6
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Parmar K, Komarow L, Ellison DW, Filippov AA, Nikolich MP, Fackler JR, Lee M, Nair A, Agrawal P, Tamma PD, Souli M, Evans SR, Greenwood-Quaintance KE, Cunningham SA, Patel R. Interlaboratory comparison of Pseudomonas aeruginosa phage susceptibility testing. J Clin Microbiol 2023; 61:e0061423. [PMID: 37962552 PMCID: PMC10729752 DOI: 10.1128/jcm.00614-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 09/25/2023] [Indexed: 11/15/2023] Open
Abstract
Standardized approaches to phage susceptibility testing (PST) are essential to inform selection of phages for study in patients with bacterial infections. There is no reference standard for assessing bacterial susceptibility to phage. We compared agreement between PST performed at three centers: two centers using a liquid assay standardized between the sites with the third, a plaque assay. Four Pseudomonas aeruginosa phages: PaWRA01ø11 (EPa11), PaWRA01ø39 (EPa39), PaWRA02ø83 (EPa83), PaWRA02ø87 (EPa87), and a cocktail of all four phages were tested against 145 P. aeruginosa isolates. Comparisons were made within measurements at the two sites performing the liquid assay and between these two sites. Agreement was assessed based on coverage probability (CP8), total deviation index, concordance correlation coefficient (CCC), measurement accuracy, and precision. For the liquid assay, there was satisfactory agreement among triplicate measurements made on different days at site 1, and high agreement based on accuracy and precision between duplicate measurements made on the same run at site 2. There was fair accuracy between measurements of the two sites performing the liquid assay, with CCCs below 0.6 for all phages tested. When compared to the plaque assay (performed once at site 3), there was less agreement between results of the liquid and plaque assays than between the two sites performing the liquid assay. Similar findings to the larger group were noted in the subset of 46 P. aeruginosa isolates from cystic fibrosis. Results of this study suggest that reproducibility of PST methods needs further development.
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Affiliation(s)
- Krupa Parmar
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lauren Komarow
- Biostatistics Center, George Washington University, Rockville, Maryland, USA
| | - Damon W. Ellison
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Andrey A. Filippov
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Mikeljon P. Nikolich
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | | | - Martin Lee
- Adaptive Phage Therapeutics Inc., Gaithersburg, Maryland, USA
| | - Anjna Nair
- Adaptive Phage Therapeutics Inc., Gaithersburg, Maryland, USA
| | - Priyesh Agrawal
- Adaptive Phage Therapeutics Inc., Gaithersburg, Maryland, USA
| | - Pranita D. Tamma
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Maria Souli
- Duke Clinical Research Institute, Durham, North Carolina, USA
| | - Scott R. Evans
- Biostatistics Center, George Washington University, Rockville, Maryland, USA
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, D.C., USA
| | - Kerryl E. Greenwood-Quaintance
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Scott A. Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - for the Antibacterial Resistance Leadership Group
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
- Biostatistics Center, George Washington University, Rockville, Maryland, USA
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
- Adaptive Phage Therapeutics Inc., Gaithersburg, Maryland, USA
- Division of Pediatric Infectious Diseases, Department of Pediatrics, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Duke Clinical Research Institute, Durham, North Carolina, USA
- Department of Biostatistics and Bioinformatics, Milken Institute School of Public Health, George Washington University, Washington, D.C., USA
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
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7
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Fang C, Dai X, Xiang L, Qiu Y, Yin M, Fu Y, Li Y, Zhang L. Isolation and characterization of three novel lytic phages against K54 serotype carbapenem-resistant hypervirulent Klebsiella pneumoniae. Front Cell Infect Microbiol 2023; 13:1265011. [PMID: 38149011 PMCID: PMC10749971 DOI: 10.3389/fcimb.2023.1265011] [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: 07/21/2023] [Accepted: 11/28/2023] [Indexed: 12/28/2023] Open
Abstract
The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) has driven us to explore alternative treatments for the limitation of antimicrobial agents. Lytic phages are considered a promising alternative treatment for CR-hvKP infection. In this study, we reported three novel lytic phages, vB_KpnA_SCNJ1-Z, vB_KpnS_SCNJ1-C, and vB_KpnM_SCNJ1-Y, against a CR-hvKP strain SCNJ1, and they possess genomes of double-stranded DNA with a size of 43,428 bp, 46,039 bp, and 50,360 bp, respectively. Phylogenetic analysis demonstrated that vB_KpnA_SCNJ1-Z belongs to the family Autographiviridae within the class Caudoviricetes, while vB_KpnS_SCNJ1-C and vB_KpnM_SCNJ1-Y are unclassified Caudoviricetes. The phages showed a narrow host range only lysing 1 of 50 tested clinical bacterial strains. The one-step growth curves and stability results showed that the phages displayed relatively short latency periods, with broad pH (pH 3-14) and thermal stabilities (20-60°C). The phages showed significant inhibition of the biofilm formation by SCNJ1 and strong antibacterial activity in vitro. In the mouse model, we demonstrated that administration of a single phage or phage cocktail significantly reduced bacteria loads in the lung, liver, and spleen, and effectively rescued mice from the infection of the SCNJ1 strain, with a survival rate of 70-80%. These findings suggested the three phages have great potential as an alternative therapy with favorable stability and strong antibacterial activity both in vivo and in vitro for the treatment of CR-hvKP infection.
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Affiliation(s)
| | | | | | | | | | | | - Ying Li
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
| | - Luhua Zhang
- The School of Basic Medical Science and Public Center of Experimental Technology, Southwest Medical University, Luzhou, Sichuan, China
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8
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Abedon ST. How Simple Maths Can Inform Our Basic Understanding of Phage Therapy. Clin Infect Dis 2023; 77:S401-S406. [PMID: 37932116 DOI: 10.1093/cid/ciad480] [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] [Indexed: 11/08/2023] Open
Abstract
Phage therapy is the application of bacterial viruses to control and, ideally, to eliminate problematic bacteria from patients. Usually employed are so-called strictly lytic phages, which upon adsorption of a bacterium should give rise to both bacterial death and bacterial lysis. This killing occurs with single-hit kinetics, resulting in relatively simple ways to mathematically model organismal-level, phage-bacterium interactions. Reviewed here are processes of phage therapy as viewed from these simpler mathematical perspectives, starting with phage dosing, continuing through phage adsorption of bacteria, and then considering the potential for phage numbers to be enhanced through in situ phage population growth. Overall, I suggest that a basic working knowledge of the underlying "simple maths" of phage therapy can be helpful toward making dosing decisions and predicting certain outcomes. This especially is during controlled in vitro experimentation but is relevant to thinking about in vivo applications as well.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio, USA
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9
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Mutti M, Moreno DS, Restrepo-Córdoba M, Visram Z, Resch G, Corsini L. Phage activity against Staphylococcus aureus is impaired in plasma and synovial fluid. Sci Rep 2023; 13:18204. [PMID: 37875544 PMCID: PMC10598271 DOI: 10.1038/s41598-023-45405-8] [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: 05/10/2023] [Accepted: 10/19/2023] [Indexed: 10/26/2023] Open
Abstract
S. aureus is a pathogen that frequently causes severe morbidity and phage therapy is being discussed as an alternative to antibiotics for the treatment of S. aureus infections. In this in vitro and animal study, we demonstrated that the activity of anti-staphylococcal phages is severely impaired in 0.5% plasma or synovial fluid. Despite phage replication in these matrices, lysis of the bacteria was slower than phage propagation, and no reduction of the bacterial population was observed. The inhibition of the phages associated with a reduction in phage adsorption, quantified to 99% at 10% plasma. S. aureus is known to bind multiple coagulation factors, resulting in the formation of aggregates and blood clots that might protect the bacterium from the phages. Here, we show that purified fibrinogen at a sub-physiological concentration of 0.4 mg/ml is sufficient to impair phage activity. In contrast, dissolution of the clots by tissue plasminogen activator (tPA) partially restored phage activity. Consistent with these in vitro findings, phage treatment did not reduce bacterial burdens in a neutropenic mouse S. aureus thigh infection model. In summary, phage treatment of S. aureus infections inside the body may be fundamentally challenging, and more investigation is needed prior to proceeding to in-human trials.
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Affiliation(s)
| | | | | | | | - Grégory Resch
- Center for Research and Innovation in Clinical Pharmaceutical Sciences (CRISP), Lausanne Hospital (CHUV), Lausanne, Switzerland
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10
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Han M, Niu X, Xiong G, Ruan C, Chen G, Wu H, Liu Y, Zhu K, Wang G. Isolation, characterization and genomic analysis of the novel Arthrobacter sp. phage SWEP2. Arch Virol 2023; 168:276. [PMID: 37864004 DOI: 10.1007/s00705-023-05898-0] [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: 03/25/2023] [Accepted: 09/01/2023] [Indexed: 10/22/2023]
Abstract
A new virulent phage, SWEP2, infecting the Arthrobacter sp. 5B strain, was isolated from black soil samples in northeastern China. SWEP2 has a latent period of 80 min and a burst size of 45 PFU (evaluated at an MOI of 0.1). Genomic analysis revealed that the 43,398-bp dsDNA genome of phage SWEP2 contains 64 open reading frames (ORFs) and one tRNA gene. Phylogenetic analysis indicated a close relationship between SWEP2 and Arthrobacter phage Liebe, with 82.98% identity and a query coverage of 48%. Based on its distinct phenotypic and genetic characteristics, SWEP2 is identified as a novel Arthrobacter phage.
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Affiliation(s)
- Miao Han
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xinyao Niu
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Guangzhou Xiong
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Chujin Ruan
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
- Department of Environmental Microbiology, Eawag, 8600, Dübendorf, Switzerland
| | - Guowei Chen
- School of Civil and Hydraulic Engineering, Hefei University of Technology, Hefei, 230009, China
| | - Hanqing Wu
- The Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha, 410125, China
| | - Ying Liu
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Kun Zhu
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Gang Wang
- College of Land Science and Technology, China Agricultural University, Beijing, 100193, China.
- National Black Soil and Agriculture Research, China Agricultural University, Beijing, 100193, China.
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11
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Xuan G, Zhao G, Wang Y, Su Q, Wang J, Lin H. Complete genome analysis and biological characterization of a novel phage vB_CP_qdyz_P5 with lytic activity against Clostridium perfringens. Microb Pathog 2023; 183:106279. [PMID: 37549798 DOI: 10.1016/j.micpath.2023.106279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/30/2023] [Accepted: 07/31/2023] [Indexed: 08/09/2023]
Abstract
Clostridium perfringens, a common foodborne pathogen, exhibit high-stress resistance. The prevailing reliance on antibiotics in the farming industry for its prevention and control has led to increasing concerns over antibiotic residue and bacterial resistance. Bacteriophages that possess specific lytic activity against C. perfringens are of significant interest. Here, a novel C. perfringens phage, named vB_CP_qdyz_P5, was isolated and characterized. The phage displayed high stability at temperatures below 70 °C and pH levels ranging from 4 to 12. Genome analysis revealed that vB_CP_qdyz_P5 has a double-stand DNA of 18,888 bp with a G + C composition of 28.8%. Among the 27 identified opening reading frames (ORFs), eight were found to be functional genes. BLASTn analysis showed that vB_CP_qdyz_P5 is closely related to phage DCp1, with a genome homology coverage of 83%. Phylogenetic analysis indicated that vB_CP_qdyz_P5 may be a novel phage of the family Guelinviridae, Susfortunavirus. This study provides important preliminary information for further research on the potential use of vB_CP_qdyz_P5 in protecting against C. perfringens and maintaining intestinal health.
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Affiliation(s)
- Guanhua Xuan
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Gang Zhao
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Yue Wang
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Qiao Su
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
| | - Jingxue Wang
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China.
| | - Hong Lin
- Food Safety Laboratory, College of Food Science and Engineering, Ocean University of China, Qingdao, 266003, China
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12
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Abedon ST. Schlesinger Nailed It! Assessing a Key Primary Pharmacodynamic Property of Phages for Phage Therapy: Virion Encounter Rates with Motionless Bacterial Targets. DRUGS AND DRUG CANDIDATES 2023; 2:673-688. [PMID: 38770155 PMCID: PMC11104014 DOI: 10.3390/ddc2030034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
Bacteriophages (phages) are viruses of bacteria and have been used as antibacterial agents now for over one-hundred years. The primary pharmacodynamics of therapeutic phages can be summed up as follows: phages at a certain concentration can reach bacteria at a certain rate, attach to bacteria that display appropriate receptors on their surfaces, infect, and (ideally) kill those now-adsorbed bacteria. Here, I consider the rate at which phages reach bacteria, during what can be dubbed as an 'extracellular search'. This search is driven by diffusion and can be described by what is known as the phage adsorption rate constant. That constant in turn is thought to be derivable from knowledge of bacterial size, virion diffusion rates, and the likelihood of phage adsorption given this diffusion-driven encounter with a bacterium. Here, I consider only the role of bacterial size in encounter rates. In 1932, Schlesinger hypothesized that bacterial size can be described as a function of cell radius (R , or R 1 ), as based on the non-phage-based theorizing of Smoluchowski (1917). The surface area of a cell-what is actually encountered-varies however instead as a function R 2 . Here, I both provide and review evidence indicating that Schlesinger's assertion seems to have been correct.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA
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13
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Riber L, Carstens AB, Dougherty PE, Roy C, Willenbücher K, Hille F, Franz CMAP, Hansen LH. Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus. Microorganisms 2023; 11:1831. [PMID: 37513003 PMCID: PMC10385605 DOI: 10.3390/microorganisms11071831] [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: 06/24/2023] [Revised: 07/14/2023] [Accepted: 07/16/2023] [Indexed: 07/30/2023] Open
Abstract
Bacteriophages are viral agents that infect and replicate within bacterial cells. Despite the increasing importance of phage ecology, environmental phages-particularly those targeting phyllosphere-associated bacteria-remain underexplored, and current genomic databases lack high-quality phage genome sequences linked to specific environmentally important bacteria, such as the ubiquitous sphingomonads. Here, we isolated three novel phages from a Danish wastewater treatment facility. Notably, these phages are among the first discovered to target and regulate a Sphingomonas genus within the wheat phyllosphere microbiome. Two of the phages displayed a non-prolate Siphovirus morphotype and demonstrated a narrow host range when tested against additional Sphingomonas strains. Intergenomic studies revealed limited nucleotide sequence similarity within the isolated phage genomes and to publicly available metagenome data of their closest relatives. Particularly intriguing was the limited homology observed between the DNA polymerase encoding genes of the isolated phages and their closest relatives. Based on these findings, we propose three newly identified genera of viruses: Longusvirus carli, Vexovirus birtae, and Molestusvirus kimi, following the latest ICTV binomial nomenclature for virus species. These results contribute to our current understanding of phage genetic diversity in natural environments and hold promising implications for phage applications in phyllosphere microbiome manipulation strategies.
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Affiliation(s)
- Leise Riber
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Alexander Byth Carstens
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Peter Erdmann Dougherty
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Chayan Roy
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
| | - Katharina Willenbücher
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Strasse 1, 24103 Kiel, Germany
| | - Frank Hille
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Strasse 1, 24103 Kiel, Germany
| | - Charles M A P Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Hermann-Weigmann-Strasse 1, 24103 Kiel, Germany
| | - Lars Hestbjerg Hansen
- Department of Plant and Environmental Sciences, University of Copenhagen, Thorvaldsensvej 40, DK-1871 Frederiksberg, Denmark
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14
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Laguna-Castro M, Rodríguez-Moreno A, Llorente E, Lázaro E. The balance between fitness advantages and costs drives adaptation of bacteriophage Qβ to changes in host density at different temperatures. Front Microbiol 2023; 14:1197085. [PMID: 37303783 PMCID: PMC10248866 DOI: 10.3389/fmicb.2023.1197085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 05/12/2023] [Indexed: 06/13/2023] Open
Abstract
Introduction Host density is one of the main factors affecting the infective capacity of viruses. When host density is low, it is more difficult for the virus to find a susceptible cell, which increases its probability of being damaged by the physicochemical agents of the environment. Nevertheless, viruses can adapt to variations in host density through different strategies that depend on the particular characteristics of the life cycle of each virus. In a previous work, using the bacteriophage Qβ as an experimental model, we found that when bacterial density was lower than optimal the virus increased its capacity to penetrate into the bacteria through a mutation in the minor capsid protein (A1) that is not described to interact with the cell receptor. Results Here we show that the adaptive pathway followed by Qβ in the face of similar variations in host density depends on environmental temperature. When the value for this parameter is lower than optimal (30°C), the mutation selected is the same as at the optimal temperature (37°C). However, when temperature increases to 43°C, the mutation selected is located in a different protein (A2), which is involved both in the interaction with the cell receptor and in the process of viral progeny release. The new mutation increases the entry of the phage into the bacteria at the three temperatures assayed. However, it also considerably increases the latent period at 30 and 37°C, which is probably the reason why it is not selected at these temperatures. Conclusion The conclusion is that the adaptive strategies followed by bacteriophage Qβ, and probably other viruses, in the face of variations in host density depend not only on their advantages at this selective pressure, but also on the fitness costs that particular mutations may present in function of the rest of environmental parameters that influence viral replication and stability.
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15
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Abedon ST. Bacteriophage Adsorption: Likelihood of Virion Encounter with Bacteria and Other Factors Affecting Rates. Antibiotics (Basel) 2023; 12:723. [PMID: 37107086 PMCID: PMC10135360 DOI: 10.3390/antibiotics12040723] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 03/29/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
For ideal gasses, the likelihood of collision of two molecules is a function of concentrations as well as environmental factors such as temperature. This too is the case for particles diffusing within liquids. Two such particles are bacteria and their viruses, the latter called bacteriophages or phages. Here, I review the basic process of predicting the likelihoods of phage collision with bacteria. This is a key step governing rates of phage-virion adsorption to their bacterial hosts, thereby underlying a large fraction of the potential for a given phage concentration to affect a susceptible bacterial population. Understanding what can influence those rates is very relevant to appreciating both phage ecology and the phage therapy of bacterial infections, i.e., where phages are used to augment or replace antibiotics; so too adsorption rates are highly important for predicting the potential for phage-mediated biological control of environmental bacteria. Particularly emphasized here, however, are numerous complications on phage adsorption rates beyond as dictated by the ideals of standard adsorption theory. These include movements other than due to diffusion, various hindrances to diffusive movement, and the influence of assorted heterogeneities. Considered chiefly are the biological consequences of these various phenomena rather than their mathematical underpinnings.
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16
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Aminolipids elicit functional trade-offs between competitiveness and bacteriophage attachment in Ruegeria pomeroyi. THE ISME JOURNAL 2023; 17:315-325. [PMID: 36477724 PMCID: PMC9938194 DOI: 10.1038/s41396-022-01346-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 11/17/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022]
Abstract
Lipids play a crucial role in maintaining cell integrity and homeostasis with the surrounding environment. Cosmopolitan marine roseobacter clade (MRC) and SAR11 clade bacteria are unique in that, in addition to glycerophospholipids, they also produce an array of amino acid-containing lipids that are conjugated with beta-hydroxy fatty acids through an amide bond. Two of these aminolipids, the ornithine aminolipid (OL) and the glutamine aminolipid (QL), are synthesized using the O-acetyltransferase OlsA. Here, we demonstrate that OL and QL are present in both the inner and outer membranes of the Gram-negative MRC bacterium Ruegeria pomeroyi DSS-3. In an olsA mutant, loss of these aminolipids is compensated by a concurrent increase in glycerophospholipids. The inability to produce aminolipids caused significant changes in the membrane proteome, with the membrane being less permeable and key nutrient transporters being downregulated while proteins involved in the membrane stress response were upregulated. Indeed, the import of 14C-labelled choline and dimethylsulfoniopropionate, as a proxy for the transport of key marine nutrients across membranes, was significantly impaired in the olsA mutant. Moreover, the olsA mutant was significantly less competitive than the wild type (WT) being unable to compete with the WT strain in co-culture. However, the olsA mutant unable to synthesize these aminolipids is less susceptible to phage attachment. Together, these data reveal a critical role for aminolipids in the ecophysiology of this important clade of marine bacteria and a trade-off between growth and avoidance of bacteriophage attachment.
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17
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Characteristics of Environmental Klebsiella pneumoniae and Klebsiella oxytoca Bacteriophages and Their Therapeutic Applications. Pharmaceutics 2023; 15:pharmaceutics15020434. [PMID: 36839755 PMCID: PMC9960720 DOI: 10.3390/pharmaceutics15020434] [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: 12/19/2022] [Revised: 01/23/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
In recent years, multidrug-resistant (MDR) strains of Klebsiella pneumoniae have spread globally, being responsible for the occurrence and severity of nosocomial infections. The NDM-1-kp, VIM-1 carbapenemase-producing isolates as well as extended-spectrum beta lactamase-producing (ESBL) isolates along with Klebsiella oxytoca strains have become emerging pathogens. Due to the growing problem of antibiotic resistance, bacteriophage therapy may be a potential alternative to combat such multidrug-resistant Klebsiella strains. Here, we present the results of a long-term study on the isolation and biology of bacteriophages active against K. pneumoniae, as well as K. oxytoca strains. We evaluated biological properties, morphology, host specificity, lytic spectrum and sensitivity of these phages to chemical agents along with their life cycle parameters such as adsorption, latent period, and burst size. Phages designated by us, vB_KpnM-52N (Kpn52N) and VB_KpnM-53N (Kpn53N), demonstrated relatively broad lytic spectra among tested Klebsiella strains, high burst size, adsorption rates and stability, which makes them promising candidates for therapeutic purposes. We also examined selected Klebsiella phages from our historical collection. Notably, one phage isolated nearly 60 years ago was successfully used in purulent cerebrospinal meningitis in a new-born and has maintained lytic activity to this day. Genomic sequences of selected phages were determined and analyzed. The phages of the sequenced genomes belong to the Slopekvirus and Jiaodavirus genus, a group of phages related to T4 at the family level. They share several features of T4 making them suitable for antibacterial therapies: the obligatorily lytic lifestyle, a lack of homologs of known virulence or antibiotic resistance genes, and a battery of enzymes degrading host DNA at infection.
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18
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Abedon ST. Ecology and Evolutionary Biology of Hindering Phage Therapy: The Phage Tolerance vs. Phage Resistance of Bacterial Biofilms. Antibiotics (Basel) 2023; 12:245. [PMID: 36830158 PMCID: PMC9952518 DOI: 10.3390/antibiotics12020245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/17/2023] [Accepted: 01/19/2023] [Indexed: 01/27/2023] Open
Abstract
As with antibiotics, we can differentiate various acquired mechanisms of bacteria-mediated inhibition of the action of bacterial viruses (phages or bacteriophages) into ones of tolerance vs. resistance. These also, respectively, may be distinguished as physiological insensitivities (or protections) vs. resistance mutations, phenotypic resistance vs. genotypic resistance, temporary vs. more permanent mechanisms, and ecologically vs. also near-term evolutionarily motivated functions. These phenomena can result from multiple distinct molecular mechanisms, many of which for bacterial tolerance of phages are associated with bacterial biofilms (as is also the case for the bacterial tolerance of antibiotics). The resulting inhibitions are relevant from an applied perspective because of their potential to thwart phage-based treatments of bacterial infections, i.e., phage therapies, as well as their potential to interfere more generally with approaches to the phage-based biological control of bacterial biofilms. In other words, given the generally low toxicity of properly chosen therapeutic phages, it is a combination of phage tolerance and phage resistance, as displayed by targeted bacteria, that seems to represent the greatest impediments to phage therapy's success. Here I explore general concepts of bacterial tolerance of vs. bacterial resistance to phages, particularly as they may be considered in association with bacterial biofilms.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA
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19
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Dong Z, Wang K, Peng D, Yu C. Characteristics and complete genome analysis of the novel virulent phage Bfsp1 infecting Cytobacillus firmus. Arch Virol 2023; 168:56. [PMID: 36617608 DOI: 10.1007/s00705-022-05660-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 10/20/2022] [Indexed: 01/10/2023]
Abstract
We isolated, identified, and characterised Bfsp1, a novel virulent phage of Cytobacillus firmus. Morphologically, Bfsp1 is similar to phi29-like phages. The linear, double-stranded DNA genome of Bfsp1 is 22,320 bp in length, has a GC content of 36.06%, and has 10-bp inverted terminal repeats. The genome contains 33 open reading frames, and functions of 15 of them were predicted. Comparative genome analysis showed that Bfsp1 is distinct from other known phages, and this was confirmed by phylogenetic analysis. Morphological, genomic, and phylogenetic data indicated that Bfsp1 is a novel member of the family Salasmaviridae.
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Affiliation(s)
- Zhaoxia Dong
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China
| | - Kai Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
| | - Cui Yu
- Industrial Crops Institute of Hubei Academy of Agricultural Sciences, Wuhan, 430064, Hubei, China.
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20
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Effective Therapeutic Options for Melioidosis: Antibiotics versus Phage Therapy. Pathogens 2022; 12:pathogens12010011. [PMID: 36678359 PMCID: PMC9863960 DOI: 10.3390/pathogens12010011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/08/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Melioidosis, also known as Whitmore's disease, is a potentially fatal infection caused by the Gram-negative bacteria Burkholderia pseudomallei with a mortality rate of 10-50%. The condition is a "glanders-like" illness prevalent in Southeast Asian and Northern Australian regions and can affect humans, animals, and sometimes plants. Melioidosis received the epithet "the great mimicker" owing to its vast spectrum of non-specific clinical manifestations, such as localised abscesses, septicaemia, pneumonia, septic arthritis, osteomyelitis, and encephalomyelitis, which often lead to misdiagnosis and ineffective treatment. To date, antibiotics remain the backbone of melioidosis treatment, which includes intravenous therapy with ceftazidime or meropenem, followed by oral therapy with TMP-SMX or amoxicillin/clavulanic acid and supported by adjunctive treatment. However, bacteria have developed resistance to a series of antibiotics, including clinically significant ones, during treatment. Therefore, phage therapy has gained unprecedented interest and has been proposed as an alternative treatment. Although no effective phage therapy has been published, the findings of experimental phage therapies suggest that the concept could be feasible. This article reviews the benefits and limitations of antibiotics and phage therapy in terms of established regimens, bacterial resistance, host specificity, and biofilm degradation.
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21
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Yuan S, Shi J, Jiang J, Ma Y. Genome-scale top-down strategy to generate viable genome-reduced phages. Nucleic Acids Res 2022; 50:13183-13197. [PMID: 36511873 PMCID: PMC9825161 DOI: 10.1093/nar/gkac1168] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/18/2022] [Accepted: 11/23/2022] [Indexed: 12/14/2022] Open
Abstract
Efforts have been made to reduce the genomes of living cells, but phage genome reduction remains challenging. It is of great interest to investigate whether genome reduction can make phages obtain new infectious properties. We developed a CRISPR/Cas9-based iterative phage genome reduction (CiPGr) approach and applied this to four distinct phages, thereby obtaining heterogeneous genome-reduced mutants. We isolated and sequenced 200 mutants with loss of up to 8-23% (3.3-35 kbp) of the original sequences. This allowed the identification of non-essential genes for phage propagation, although loss of these genes is mostly detrimental to phage fitness to various degrees. Notwithstanding this, mutants with higher infectious efficiency than their parental strains were characterized, indicating a trade-off between genome reduction and infectious fitness for phages. In conclusion, this study provides a foundation for future work to leverage the information generated by CiPGr in phage synthetic biology research.
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Affiliation(s)
- Shengjian Yuan
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Juan Shi
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Jianrong Jiang
- Shenzhen Key Laboratory of Synthetic Genomics, Guangdong Provincial Key Laboratory of Synthetic Genomics, CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Yingfei Ma
- To whom correspondence should be addressed. Tel: +86 755 8639 2674;
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22
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Mirzaei A, Wagemans J, Nasr Esfahani B, Lavigne R, Moghim S. A Phage Cocktail To Control Surface Colonization by Proteus mirabilis in Catheter-Associated Urinary Tract Infections. Microbiol Spectr 2022; 10:e0209222. [PMID: 36194151 PMCID: PMC9602741 DOI: 10.1128/spectrum.02092-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Accepted: 09/02/2022] [Indexed: 12/31/2022] Open
Abstract
Proteus mirabilis is a biofilm-forming bacterium and one of the most common causes of catheter-associated urinary tract infections (CAUTIs). The rapid spread of multidrug-resistant P. mirabilis represents a severe threat to management of nosocomial infections. This study aimed to isolate a potent phage cocktail and assess its potential to control urinary tract infections caused by biofilm-forming P. mirabilis. Two lytic phages, Isf-Pm1 and Isf-Pm2, were isolated and characterized by proteome analysis, transmission electron microscopy, and whole-genome sequencing. The host range and effect of the phage cocktail to reduce the biofilm formation were assessed by a cell adhesion assay in Vero cells and a phantom bladder model. The samples treated with the phage cocktail showed a significant reduction (65%) in the biofilm mass. Anti-quorum sensing and quantitative real-time PCR assays were also used to assess the amounts of transcription of genes involved in quorum sensing and biofilm formation. Furthermore, the phage-treated samples showed a downregulation of genes involved in the biofilm formation. In conclusion, these results highlight the efficacy of two isolated phages to control the biofilms produced by P. mirabilis CAUTIs. IMPORTANCE The rapid spread of multidrug-resistant (MDR) and extensively drug-resistant (XDR) bacterial strains and biofilm formation of bacteria have severely restricted the use of antibiotics and become a challenging issue in hospitals. Therefore, there is a necessity for alternative or complementary treatment measures, such as the use of virulent bacteriophages (phages), as effective therapeutic strategies.
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Affiliation(s)
- Arezoo Mirzaei
- Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | | | - Bahram Nasr Esfahani
- Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Rob Lavigne
- Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Sharareh Moghim
- Department of Bacteriology and Virology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
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23
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Daubie V, Chalhoub H, Blasdel B, Dahma H, Merabishvili M, Glonti T, De Vos N, Quintens J, Pirnay JP, Hallin M, Vandenberg O. Determination of phage susceptibility as a clinical diagnostic tool: A routine perspective. Front Cell Infect Microbiol 2022; 12:1000721. [PMID: 36211951 PMCID: PMC9532704 DOI: 10.3389/fcimb.2022.1000721] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/30/2022] [Indexed: 11/13/2022] Open
Abstract
As the global burden of disease caused by multidrug resistant bacteria is a major source of concern, credible clinical alternatives to antibiotic therapy, such as personalized phage therapy, are actively explored. Although phage therapy has been used for more than a century, the issue of an easy to implement diagnostic tool for determining phage susceptibility that meets current routine clinical needs is still open. In this Review, we summarize the existing methods used for determining phage activity on bacteria, including the three reference methods: the spot test, the double agar overlay plaque assay, and the Appelmans method. The first two methods rely on the principle of challenging the overnight growth of a lawn of bacteria in an agar matrix to a known relative phage to bacteria concentration and represent good screening tools to determine if the tested phage can be used for a “passive” and or “active” treatment. Beside these methods, several techniques, based on “real-time” growth kinetics assays (GKA) have been developed or are under development. They all monitor the growth of clinical isolates in the presence of phages, but use various detection methods, from classical optical density to more sophisticated techniques such as computer-assisted imagery, flow-cytometry, quantitative real-time polymerase chain reaction (qPCR) or metabolic indicators. Practical considerations as well as information provided about phage activity are reviewed for each technique. Finally, we also discuss the analytical and interpretative requirements for the implementation of a phage susceptibility testing tool in routine clinical microbiology.
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Affiliation(s)
- Valéry Daubie
- Innovation and Business Development Unit, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
- Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Houssein Chalhoub
- Innovation and Business Development Unit, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Bob Blasdel
- R&D department, Vesale Bioscience, Noville-sur-Mehaigne, Belgium
| | - Hafid Dahma
- Department of Microbiology, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Maya Merabishvili
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Tea Glonti
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Nathalie De Vos
- Department of Clinical Chemistry, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
| | - Johan Quintens
- R&D department, Vesale Bioscience, Noville-sur-Mehaigne, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, Brussels, Belgium
| | - Marie Hallin
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Olivier Vandenberg
- Innovation and Business Development Unit, LHUB-ULB, Université Libre de Bruxelles, Brussels, Belgium
- Centre for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, United Kingdom
- *Correspondence: Olivier Vandenberg,
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24
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Complete Genome Sequence of Dickeya chrysanthemi Bacteriophage DchS19. Microbiol Resour Announc 2022; 11:e0080022. [PMID: 36102644 PMCID: PMC9583810 DOI: 10.1128/mra.00800-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized the complete genome of a lytic Dickeya chrysanthemi bacteriophage, DchS19, which was isolated from a soil sample in Sungai Petani, Kedah, Malaysia. The phage, from the Autographviridae family, has a 39,149-bp double-stranded DNA genome containing 49 protein-coding genes and shares 94.65% average nucleotide identity with Erwinia phage pEp_SNUABM_12.
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25
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Van Cauwenberghe J, Santamaría RI, Bustos P, González V. Novel lineages of single-stranded DNA phages that coevolved with the symbiotic bacteria Rhizobium. Front Microbiol 2022; 13:990394. [PMID: 36177468 PMCID: PMC9512667 DOI: 10.3389/fmicb.2022.990394] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 08/19/2022] [Indexed: 11/27/2022] Open
Abstract
This study describes novel single-stranded DNA phages isolated from common bean agriculture soils by infection of the nitrogen-fixing symbiotic bacteria Rhizobium etli and R. phaseoli. A total of 29 phages analyzed have 4.3–6 kb genomes in size and GC 59–60%. They belong to different clades unrelated to other Microviridae subfamilies. Three-dimensional models of the major capsid protein (MCP) showed a conserved β-barrel structural “jelly-roll” fold. A variable-length loop in the MCPs distinguished three Rhizobium microvirus groups. Microviridae subfamilies were consistent with viral clusters determined by the protein-sharing network. All viral clusters, except for Bullavirinae, included mostly microviruses identified in metagenomes from distinct ecosystems. Two Rhizobium microvirus clusters, chaparroviruses, and chicoviruses, were included within large viral unknown clusters with microvirus genomes identified in diverse metagenomes. A third Rhizobium microvirus cluster belonged to the subfamily Amoyvirinae. Phylogenetic analysis of the MCP confirms the divergence of the Rhizobium microviruses into separate clades. The phylogeny of the bacterial hosts matches the microvirus MCP phylogeny, suggesting a coevolutionary history between the phages and their bacterial host. This study provided essential biological information on cultivated microvirus for understanding the evolution and ecological diversification of the Microviridae family in diverse microbial ecosystems.
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Affiliation(s)
- Jannick Van Cauwenberghe
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
- Department of Integrative Biology, University of California, Berkeley, CA, United States
- *Correspondence: Jannick Van Cauwenberghe,
| | - Rosa I. Santamaría
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
| | - Patricia Bustos
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
| | - Víctor González
- Centro de Ciencias Genómicas, Universidad Nacional Autonóma de México, Cuernavaca, Mexico
- Víctor González,
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26
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O’Hara BJ, Alam M, Ng WL. The Vibrio cholerae Seventh Pandemic Islands act in tandem to defend against a circulating phage. PLoS Genet 2022; 18:e1010250. [PMID: 36026491 PMCID: PMC9455884 DOI: 10.1371/journal.pgen.1010250] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Revised: 09/08/2022] [Accepted: 08/02/2022] [Indexed: 11/19/2022] Open
Abstract
The current circulating pandemic El Tor biotype of Vibrio cholerae has persisted for over sixty years and is characterized by its acquisition of two unique genomic islands called the Vibrio Seventh Pandemic Islands 1 and 2 (VSP-I and VSP-II). However, the functions of most of the genes on VSP-I and VSP-II are unknown and the advantages realized by El Tor through these two islands are not clear. Recent studies have broadly implicated these two mobile genetic elements with phage defense. Still, protection against phage infection through these islands has not been observed directly in any V. cholerae El Tor biotype. Here we report the isolation of a circulating phage from a cholera patient stool sample and demonstrate that propagation of this phage in its native host is inhibited by elements in both VSP-I and VSP-II, providing direct evidence for the role of these genomic islands in phage defense. Moreover, we show that these defense systems are regulated by quorum sensing and active only at certain cell densities. Finally, we have isolated a naturally occurring phage variant that is resistant to the defense conferred by the VSP islands, illustrating the countermeasures used by phages to evade these defense mechanisms. Together, this work demonstrates a functional role for the VSPs in V. cholerae and highlights the key regulatory and mechanistic insights that can be gained by studying anti-phage systems in their native contexts. The current pandemic strain of Vibrio cholerae carries two unique genomic islands. How these two islands confer evolutionary advantage to the pathogen is unknown. We show here the identification of a circulating phage that is sensitive to the defense systems present on these two islands and demonstrate how phage variants can evade these defenses. Our studies provide the first direct evidence showing the importance of these genomic islands in defending against phage in their native environments; and in doing so provide novel insight into the mechanisms of these highly conserved defense elements.
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Affiliation(s)
- Brendan J. O’Hara
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Program of Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Munirul Alam
- Infectious Diseases Division, International Center for Diarrheal Disease Research, Dhaka, Bangladesh
| | - Wai-Leung Ng
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Program of Molecular Microbiology, Graduate School of Biomedical Sciences, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- * E-mail:
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27
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Minimizing Foaming and Bulking in Activated Sludge with Bacteriophage Treatment: A Review of Mathematical Modeling. Processes (Basel) 2022. [DOI: 10.3390/pr10081600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The interest in the ability of phages to control bacterial populations has extended from medical applications into the fields of agriculture, aquaculture, and the food industry. In particular, several authors have proposed using bacteriophages as an alternative method to control foaming and bulking in wastewater treatment. This strategy has shown successful results at the laboratory scale. However, this technology is still in development, and there are several challenges to overcome before bacteriophages can be widely used to control foaming and bulking in pilot or larger-scale treatment plants. Several models of the infection mechanisms in individual bacteria–phage pairs have been reported, i.e., for controlled systems with only one bacterium species in the presence of one phage species. However, activated sludge treatment systems largely differ from this situation, which opens a large horizon for future research. Mathematical models will play a key role in this development process, and this review offers an overview of the proposed models: their applications, potential, and challenges. A particular focus is placed on the model properties, such as parameter identifiability and states’ observability, which are essential for process prediction, monitoring, or dynamic optimization.
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28
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Zhou Y, Xu D, Yu H, Han J, Liu W, Qu D. Encapsulation of Salmonella phage SL01 in alginate/carrageenan microcapsules as a delivery system and its application in vitro. Front Microbiol 2022; 13:906103. [PMID: 35992667 PMCID: PMC9386268 DOI: 10.3389/fmicb.2022.906103] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 06/29/2022] [Indexed: 11/17/2022] Open
Abstract
Phages can be used successfully to treat pathogenic bacteria including zoonotic pathogens that colonize the intestines of animals and humans. However, low pH and digestive enzyme activity under harsh gastric conditions affect phage viability, thereby reducing their effectiveness. In this study, alginate (ALG)/κ-carrageenan (CG) microcapsules were developed to encapsulate and release phage under simulated gastrointestinal conditions. The effects of ALG and CG concentrations on the encapsulation and loading efficiency of microcapsules, as well as the release behavior and antibacterial effects of microcapsules in simulating human intestinal pH and temperature, were investigated. Based on various indicators, when the concentration of ALG and CG were 2.0 and 0.3%, respectively, the obtained microcapsules have high encapsulation efficiency, strong protection, and high release efficiency in simulated intestinal fluid. This effect is attributed to the formation of a more tightly packed biopolymer network within the composite microcapsules based on the measurements of their microstructure properties. Bead-encapsulation is a promising, reliable, and cost-effective method for the functional delivery of phage targeting intestinal bacteria.
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Affiliation(s)
- Yuqiao Zhou
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Dingting Xu
- The Second Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, China
| | - Haijie Yu
- Jiaxing Vocational Technical College, Jiaxing, China
| | - Jianzhong Han
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Weilin Liu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Daofeng Qu
- School of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
- *Correspondence: Daofeng Qu,
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29
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Schumann AR, Sue AD, Roach DR. Hypoxia Increases the Tempo of Phage Resistance and Mutational Bottlenecking of Pseudomonas aeruginosa. Front Microbiol 2022; 13:905343. [PMID: 35979493 PMCID: PMC9376454 DOI: 10.3389/fmicb.2022.905343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Accepted: 06/16/2022] [Indexed: 11/23/2022] Open
Abstract
Viruses that infect bacteria (i.e., phages) are abundant and widespread in the human body, and new anti-infective approaches such as phage therapy are essential for the future of effective medicine. Our understanding of microenvironmental factors such as tissue oxygen availability at the site of phage-bacteria interaction remains limited, and it is unknown whether evolved resistance is sculpted differentially under normoxia vs. hypoxia. We, therefore, analyzed the phage-bacteria interaction landscape via adsorption, one-step, time-kill dynamics, and genetic evolution under both normoxia and hypoxia. This revealed that adsorption of phages to Pseudomonas aeruginosa decreased under 14% environmental oxygen (i.e., hypoxia), but phage time-kill and one-step growth kinetics were not further influenced. Tracking the adaptation of P. aeruginosa to phages uncovered a higher frequency of phage resistance and constrained types of spontaneous mutation under hypoxia. Given the interest in developing phage therapies, developing our understanding of the phage-pathogen interaction under microenvironmental conditions resembling those in the body offers insight into possible strategies to overcome multidrug-resistant (MDR) bacteria.
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Affiliation(s)
- Ashley R. Schumann
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Andrew D. Sue
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Dwayne R. Roach
- Department of Biology, San Diego State University, San Diego, CA, United States
- Viral Information Institute, San Diego State University, San Diego, CA, United States
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30
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Wang K, Chen D, Liu Q, Zhu P, Sun M, Peng D. Isolation and Characterization of Novel Lytic Bacteriophage vB_RsoP_BMB50 infecting Ralstonia solanacearum. Curr Microbiol 2022; 79:245. [PMID: 35834130 DOI: 10.1007/s00284-022-02940-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 06/17/2022] [Indexed: 11/25/2022]
Abstract
Ralstonia solanacearum is a soil-borne phytopathogen, and it can cause bacterial wilt disease in a variety of key crops around the world, thus resulting in enormous financial losses. However, there is a lack of effective, green, and safe prevention and control measures against increasingly devastating bacterial wilt disease. Bacteriophages (phages) are considered as potential biocontrol agents against bacterial wilt disease. Although many phages infecting R. solanacearum have been isolated, so far, these Ralstonia phages are still insufficient to deal with the diversity of the bacteria of R. solanacearum. In this study, a novel lytic bacteriophage vB_RsoP_BMB50 infecting multiple R. solanacearum was isolated from tomato fields in Dalian, China. Transmission electron microscopy and genomics analysis indicated that vB_RsoP_BMB50 belonged to the subfamily Okabevirinae, Autographiviridae family, and order Caudovirales, and it comprised a double-stranded DNA with a full length of 43,665 bp and a mean G+C content of 61.79%, containing 53 open reading frames (ORFs). This novel phage exhibited a large burst size, high temperature stability (4-50 °C), and strong pH tolerance (pH 5-10). Comparative analyses and phylogenetic analyses revealed that vB_RsoP_BMB50 represented a novel Ralstonia phage genus since it exhibited a low sequence similarity to other phages in the GenBank database. Due to its broad lytic spectrum, high thermal stability, and strong pH tolerance, vB_RsoP_BMB50 is considered as an effective candidate biocontrol agent against bacterial wilt disease caused by R. solanacearum.
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Affiliation(s)
- Kai Wang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Dawei Chen
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Quanrong Liu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Pengfei Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Ming Sun
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Donghai Peng
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, Hubei, China.
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31
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Yuanyuan N, Xiaobo Y, Shang W, Yutong Y, Hongrui Z, Chenyu L, Bin X, Xi Z, Chen Z, Zhiqiang S, Jingfeng W, Yun L, Pingfeng Y, Zhigang Q. Isolation and characterization of two homolog phages infecting Pseudomonas aeruginosa. Front Microbiol 2022; 13:946251. [PMID: 35935197 PMCID: PMC9348578 DOI: 10.3389/fmicb.2022.946251] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 06/24/2022] [Indexed: 12/02/2022] Open
Abstract
Bacteriophages (phages) are capable of infecting specific bacteria, and therefore can be used as a biological control agent to control bacteria-induced animal, plant, and human diseases. In this study, two homolog phages (named PPAY and PPAT) that infect Pseudomonas aeruginosa PAO1 were isolated and characterized. The results of the phage plaque assay showed that PPAT plaques were transparent dots, while the PPAY plaques were translucent dots with a halo. Transmission electron microscopy results showed that PPAT (65 nm) and PPAY (60 nm) strains are similar in size and have an icosahedral head and a short tail. Therefore, these belong to the short-tailed phage family Podoviridae. One-step growth curves revealed the latent period of 20 min and burst time of 30 min for PPAT and PPAY. The burst size of PPAT (953 PFUs/infected cell) was higher than that of PPAY (457 PFUs/infected cell). Also, the adsorption rate constant of PPAT (5.97 × 10−7 ml/min) was higher than that of PPAY (1.32 × 10−7 ml/min) at 5 min. Whole-genome sequencing of phages was carried out using the Illumina HiSeq platform. The genomes of PPAT and PPAY have 54,888 and 50,154 bp, respectively. Only 17 of the 352 predicted ORFs of PPAT could be matched to homologous genes of known function. Likewise, among the 351 predicted ORFs of PPAY, only 18 ORFs could be matched to genes of established functions. Homology and evolutionary analysis indicated that PPAT and PPAY are closely related to PA11. The presence of tail fiber proteins in PPAY but not in PPAT may have contributed to the halo effect of its plaque spots. In all, PPAT and PPAY, newly discovered P. aeruginosa phages, showed growth inhibitory effects on bacteria and can be used for research and clinical purposes.
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Affiliation(s)
- Niu Yuanyuan
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Yang Xiaobo
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Wang Shang
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Yang Yutong
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhou Hongrui
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Li Chenyu
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Xue Bin
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhang Xi
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Zhao Chen
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Shen Zhiqiang
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Wang Jingfeng
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
| | - Ling Yun
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- *Correspondence: Ling Yun,
| | - Yu Pingfeng
- College of Environment and Resource Sciences, Zhejiang University, Hangzhou, China
| | - Qiu Zhigang
- College of Marine Ecology and Environment, Shanghai Ocean University, Shanghai, China
- Key Laboratory of Risk Assessment and Control for Environment and Food Safety, TianJin Institute of Environmental and Operational Medicine, Tianjin, China
- Qiu Zhigang,
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32
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Phage-host coevolution in natural populations. Nat Microbiol 2022; 7:1075-1086. [PMID: 35760840 DOI: 10.1038/s41564-022-01157-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 05/23/2022] [Indexed: 01/21/2023]
Abstract
Coevolution between bacteriophages (phages) and their bacterial hosts occurs through changes in resistance and counter-resistance mechanisms. To assess phage-host evolution in wild populations, we isolated 195 Vibrio crassostreae strains and 243 vibriophages during a 5-month time series from an oyster farm and combined these isolates with existing V. crassostreae and phage isolates. Cross-infection studies of 81,926 host-phage pairs delineated a modular network where phages are best at infecting co-occurring hosts, indicating local adaptation. Successful propagation of phage is restricted by the ability to adsorb to closely related bacteria and further constrained by strain-specific defence systems. These defences are highly diverse and predominantly located on mobile genetic elements, and multiple defences are active within a single genome. We further show that epigenetic and genomic modifications enable phage to adapt to bacterial defences and alter host range. Our findings reveal that the evolution of bacterial defences and phage counter-defences is underpinned by frequent genetic exchanges with, and between, mobile genetic elements.
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33
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Abedon ST. Further Considerations on How to Improve Phage Therapy Experimentation, Practice, and Reporting: Pharmacodynamics Perspectives. PHAGE (NEW ROCHELLE, N.Y.) 2022; 3:98-111. [PMID: 36148139 PMCID: PMC9436263 DOI: 10.1089/phage.2022.0019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phage therapy uses bacterial viruses (bacteriophages) to infect and kill targeted pathogens. Approximately one decade ago, I started publishing on how possibly to improve upon phage therapy experimentation, practice, and reporting. Here, I gather and expand upon some of those suggestions. The issues emphasized are (1) that using ratios of antibacterial agents to bacteria is not how dosing is accomplished in the real world, (2) that it can be helpful to not ignore Poisson distributions as a means of either anticipating or characterizing phage therapy success, and (3) how to calculate a concept of 'inundative phage densities.' Together, these are issues of phage therapy pharmacodynamics, meaning they are ways of thinking about the potential for phage therapy treatments to be efficacious mostly independent of the details of delivery of phages to targeted bacteria. Much emphasis is placed on working with Poisson distributions to better align phage therapy with other antimicrobial treatments.
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Affiliation(s)
- Stephen T. Abedon
- Department of Microbiology, The Ohio State University, Mansfield, Ohio, USA
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34
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Rathor N, Thakur CK, Das BK, Chaudhry R. An insight into the therapeutic potential of a novel lytic Pseudomonas phage isolated from the river Ganga. J Appl Microbiol 2022; 133:1353-1362. [PMID: 35616159 DOI: 10.1111/jam.15639] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 05/23/2022] [Indexed: 11/28/2022]
Abstract
AIM Bacteriophages are effective natural antimicrobial agents against drug-resistant pathogens. Therefore, identification and detailed characterization of bacteriophages become essential to explore their therapeutic potential. This study aims to isolate and characterize a lytic bacteriophage against drug-resistant Pseudomonas aeruginosa. METHODS AND RESULTS The Pseudomonas phage AIIMS-Pa-A1, isolated from the river Ganga water against drug-resistant P. aeruginosa, showed clear lytic zone on spot assay. The phage revealed icosahedral head (58.20 nm diameter) and small tail (6.83 nm) under transmission electron microscope. The growth kinetics showed adsorption constant of 1.5×10-9 phage particles cell-1 ml-1 minute-1 and latent period of approximately 15 minutes with the burst size of 27 phages per infected cell. The whole genome sequencing depicted a GC-rich genome of 40.97kb having a lysis cassette of holin, endolysin, and Rz protein, with features of the family Autographiviridae. The comparative genome analysis, Ortho-average nucleotide identity value, and phylogenetic analysis indicated the novelty of the phage AIIMS-Pa-A1. CONCLUSIONS The study concludes that the Pseudomonas phage AIIMS-Pa-A1 is a novel member of the Autographiviridae family, truly lytic in nature for drug-resistant P. aeruginosa. SIGNIFICANCE AND IMPACT OF STUDY The Pseudomonas phage AIIMS-Pa-A1 is having promising potential for future therapeutic intervention to treat drug-resistant P. aeruginosa infections.
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Affiliation(s)
- Nisha Rathor
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Chandan Kumar Thakur
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Bimal Kumar Das
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
| | - Rama Chaudhry
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi, India
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35
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Delattre R, Seurat J, Haddad F, Nguyen TT, Gaborieau B, Kane R, Dufour N, Ricard JD, Guedj J, Debarbieux L. Combination of in vivo phage therapy data with in silico model highlights key parameters for pneumonia treatment efficacy. Cell Rep 2022; 39:110825. [PMID: 35584666 DOI: 10.1016/j.celrep.2022.110825] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 10/19/2021] [Accepted: 04/25/2022] [Indexed: 12/13/2022] Open
Abstract
The clinical (re)development of bacteriophage (phage) therapy to treat antibiotic-resistant infections faces the challenge of understanding the dynamics of phage-bacteria interactions in the in vivo context. Here, we develop a general strategy coupling in vitro and in vivo experiments with a mathematical model to characterize the interplay between phage and bacteria during pneumonia induced by a pathogenic strain of Escherichia coli. The model allows the estimation of several key parameters for phage therapeutic efficacy. In particular, it quantifies the impact of dose and route of phage administration as well as the synergism of phage and the innate immune response on bacterial clearance. Simulations predict a limited impact of the intrinsic phage characteristics in agreement with the current semi-empirical choices of phages for compassionate treatments. Model-based approaches will foster the deployment of future phage-therapy clinical trials.
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Affiliation(s)
- Raphaëlle Delattre
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris 75015, France; Université Paris Cité, INSERM U1137, IAME, Paris 75006, France
| | - Jérémy Seurat
- Université Paris Cité, INSERM U1137, IAME, Paris 75006, France
| | - Feyrouz Haddad
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris 75015, France; Université Paris Cité, INSERM U1137, IAME, Paris 75006, France
| | - Thu-Thuy Nguyen
- Université Paris Cité, INSERM U1137, IAME, Paris 75006, France
| | - Baptiste Gaborieau
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris 75015, France; Université Paris Cité, INSERM U1137, IAME, Paris 75006, France; APHP, Hôpital Louis Mourier, DMU ESPRIT, Service de Médecine Intensive Réanimation, Colombes, France
| | - Rokhaya Kane
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris 75015, France
| | - Nicolas Dufour
- Centre Hospitalier René Dubos, Médecine Intensive Réanimation, Cergy Pontoise 95503, France
| | - Jean-Damien Ricard
- Université Paris Cité, INSERM U1137, IAME, Paris 75006, France; APHP, Hôpital Louis Mourier, DMU ESPRIT, Service de Médecine Intensive Réanimation, Colombes, France
| | - Jérémie Guedj
- Université Paris Cité, INSERM U1137, IAME, Paris 75006, France.
| | - Laurent Debarbieux
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Bacteriophage Bacterium Host, Paris 75015, France.
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36
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Staes I, Bäcker LE, Simoens K, De Winter K, Marolt G, Cenens W, Wolput S, Vazquez AR, Goos P, Lavigne R, Bernaerts K, Aertsen A. Superinfection exclusion factors drive a history-dependent switch from vertical to horizontal phage transmission. Cell Rep 2022; 39:110804. [PMID: 35545039 DOI: 10.1016/j.celrep.2022.110804] [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: 10/22/2021] [Revised: 03/24/2022] [Accepted: 04/19/2022] [Indexed: 11/03/2022] Open
Abstract
Temperate bacterial viruses are commonly thought to favor vertical (lysogenic) transmission over horizontal (lytic) transmission when the virion-to-host-cell ratio is high and available host cells become scarce. In P22-infected Salmonella Typhimurium populations, however, we find that host subpopulations become lytically consumed despite high phage-to-host ratios that would normally favor lysogeny. These subpopulations originate from the proliferation of P22-free siblings that spawn off from P22-carrier cells from which they cytoplasmically inherit P22-borne superinfection exclusion factors (SEFs). In fact, we demonstrate that the gradual dilution of these SEFs in the growing subpopulation of P22-free siblings restricts the number of incoming phages, thereby imposing the perception of a low phage-to-host ratio that favors lytic development. Although their role has so far been neglected, our data indicate that phage-borne SEFs can spur complex infection dynamics and a history-dependent switch from vertical to horizontal transmission in the face of host-cell scarcity.
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Affiliation(s)
- Ines Staes
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001 Leuven, Belgium
| | - Leonard E Bäcker
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001 Leuven, Belgium
| | - Kenneth Simoens
- Department of Chemical Engineering- (Bio)chemical Reactor Engineering and Safety, Faculty of Engineering, KU Leuven, Leuven, Belgium
| | - Kjerstin De Winter
- Department of Chemical Engineering- (Bio)chemical Reactor Engineering and Safety, Faculty of Engineering, KU Leuven, Leuven, Belgium
| | - Gasper Marolt
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001 Leuven, Belgium; Department of Chemical Engineering- (Bio)chemical Reactor Engineering and Safety, Faculty of Engineering, KU Leuven, Leuven, Belgium
| | - William Cenens
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001 Leuven, Belgium
| | - Sanne Wolput
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001 Leuven, Belgium
| | - Alan R Vazquez
- Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Peter Goos
- Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium; Department of Engineering Management, University of Antwerp, Antwerp, Belgium
| | - Rob Lavigne
- Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, Leuven, Belgium
| | - Kristel Bernaerts
- Department of Chemical Engineering- (Bio)chemical Reactor Engineering and Safety, Faculty of Engineering, KU Leuven, Leuven, Belgium
| | - Abram Aertsen
- Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, Kasteelpark Arenberg 23 - bus 2457, 3001 Leuven, Belgium.
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A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens. iScience 2022; 25:104121. [PMID: 35402883 PMCID: PMC8983348 DOI: 10.1016/j.isci.2022.104121] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
At its current rate, the rise of antimicrobial-resistant (AMR) infections is predicted to paralyze our industries and healthcare facilities while becoming the leading global cause of loss of human life. With limited new antibiotics on the horizon, we need to invest in alternative solutions. Bacteriophages (phages)—viruses targeting bacteria—offer a powerful alternative approach to tackle bacterial infections. Despite recent advances in using phages to treat recalcitrant AMR infections, the field lacks systematic development of phage therapies scalable to different applications. We propose a Phage Foundry framework to establish metrics for phage characterization and to fill the knowledge and technological gaps in phage therapeutics. Coordinated investment in AMR surveillance, sampling, characterization, and data sharing procedures will enable rational exploitation of phages for treatments. A fully realized Phage Foundry will enhance the sharing of knowledge, technology, and viral reagents in an equitable manner and will accelerate the biobased economy.
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Huang S, Tian Y, Wang Y, García P, Liu B, Lu R, Wu L, Bao H, Pang M, Zhou Y, Wang R, Zhang H. The Broad Host Range Phage vB_CpeS_BG3P Is Able to Inhibit Clostridium perfringens Growth. Viruses 2022; 14:v14040676. [PMID: 35458406 PMCID: PMC9033094 DOI: 10.3390/v14040676] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 12/10/2022] Open
Abstract
Clostridium perfringens is an important pathogen for both humans and animals, causing human foodborne disease and necrotic enteritis in poultry. In the present study, a C. perfringens-specific phage, vB_CpeS_BG3P (designated as BG3P hereafter), was isolated from chicken farm sewage. Both electron microscopy and phylogenetic analysis suggested that phage BG3P is a novel phage belonging to Siphoviridae family. Phage BG3P exhibited a broad host range against different C. perfringens isolates (90.63% of strains were infected). Sequencing of the complete genome revealed a linear double-stranded DNA (43,528 bp) with 28.65% GC content. After sequence analysis, 73 open reading frames (orfs) were predicted, of which only 13 were annotated with known functions. No tRNA and virulence encoding genes were detected. It should be noted that the protein of orf 15 has 97.92% homology to C. perfringens-specific chloramphenicol resistance protein, which has not been reported for any C. perfringens phage. Phylogenetic analysis of the ssDNA binding protein demonstrated that this phage is closely related to C. perfringens phages phiSM101 and phi3626. In considering future use as an antimicrobial agent, some biological characteristics were observed, such as a good pH (3−11) stability and moderate temperature tolerance (<60 °C). Moreover, bacteriophage BG3P showed a good antimicrobial effect against C. perfringens liquid cultures. Thus, phage treatment with MOI ≥ 100 completely inhibited bacterial growth compared to untreated cultures. Although phage BG3P shows good lytic efficiency and broad host range in vitro, future development and application may need to consider removal of the chloramphenicol-like resistance gene or exploring its lysin for future antibacterial applications.
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Affiliation(s)
- Sisi Huang
- College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China;
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
| | - Yuan Tian
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yongjuan Wang
- Jiangsu Agri-animal Husbandry Vocational College, Taizhou 225300, China;
| | - Pilar García
- Dairy Research Institute of Asturias (IPLA-CSIC), 33300 Villaviciosa, Asturias, Spain;
| | - Banhong Liu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
- School of Food and Biological Engineering, Shaanxi University of Science and Technology, Xi’an 710021, China
| | - Rui Lu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Liting Wu
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
| | - Hongduo Bao
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
| | - Maoda Pang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
| | - Yan Zhou
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
| | - Ran Wang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
| | - Hui Zhang
- Jiangsu Key Laboratory for Food Quality and Safety-State Key Laboratory Cultivation Base of MOST, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (Y.T.); (B.L.); (R.L.); (L.W.); (H.B.); (M.P.); (Y.Z.); (R.W.)
- Correspondence: ; Tel.: +86-25-84391627; Fax: +86-25-84391617
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Pan L, Li D, Sun Z, Lin W, Hong B, Qin W, Xu L, Liu W, Zhou Q, Wang F, Cai R, Qian M, Tong Y. First Characterization of a Hafnia Phage Reveals Extraordinarily Large Burst Size and Unusual Plaque Polymorphism. Front Microbiol 2022; 12:754331. [PMID: 35211099 PMCID: PMC8861465 DOI: 10.3389/fmicb.2021.754331] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/20/2021] [Indexed: 01/25/2023] Open
Abstract
A unique lytic phage infecting Hafnia paralvei was isolated and identified. Hafnia phage Ca belongs to the family Autographiviridae, possessing an icosahedral head with a diameter of 55 nm and a short non-contractile tail. Unusually, the burst size of Hafnia phage Ca of 10,292 ± 1,097 plaque-forming units (PFUs)/cell is much larger than other dsDNA phages reported before. Compared to the genome of the related phage, Hafnia phage Ca genome contains extra genes including DNA mimic ocr, dGTP triphosphohydrolase inhibitor, endonuclease, endonuclease VII, and HNH homing endonuclease gene. Extraordinarily, the phage developed different sizes of plaques when a single plaque was picked out and inoculated on a double-layer Luria broth agar plate with its host. Furthermore, varied packaging tightness for the tails of Hafnia phage Ca was observed (tail length: 4.35–45.92 nm). Most of the tails appeared to be like a cone with appendages, some were dot-like, bun-like, table tennis racket handle-like, and ponytail-like. Although the complete genome of Hafnia phage Ca is 40,286 bp, an incomplete genome with a deletion of a 397-bp fragment, containing one ORF predicted as HNH homing endonuclease gene (HEG), was also found by high throughput sequencing. Most of the genome of the virus particles in large plaques is complete (>98%), while most of the genome of the virus particles in small plaques is incomplete (>98%), and the abundance of both of them in medium-sized plaques is similar (complete, 40%; incomplete, 60%). In an experiment to see if the phage could be protective to brocade carps intramuscularly injected with H. paralvei LY-23 and phage Ca, the protection rate of Hafnia phage Ca to brocade carp (Cyprinus aka Koi) against H. paralvei was 33.38% (0.01 < p < 0.05). This study highlights some new insights into the peculiar biological and genomic characteristics of phage.
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Affiliation(s)
- Lingting Pan
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Dengfeng Li
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Zhitong Sun
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wei Lin
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China.,College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Binxin Hong
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Weinan Qin
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Lihua Xu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Wencai Liu
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Qin Zhou
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Fei Wang
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Ruqian Cai
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Minhua Qian
- Key Laboratory of Marine Biotechnology, School of Marine Sciences, Ningbo University, Ningbo, China
| | - Yigang Tong
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
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40
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Habibinava F, Soleimani M, Sabouri S, Zargar M, Zolfaghari MR. Isolating and sequencing vB_Kpn_3, a lytic bacteriophage against multidrug-resistant Klebsiella pneumoniae. Future Microbiol 2022; 17:235-249. [PMID: 35152708 DOI: 10.2217/fmb-2020-0272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Phage therapy, as an effective and specific method in the treatment of multidrug-resistant (MDR) bacterial infections, has attracted the attention of many researchers. Methods and results: In this study, a double-stranded DNA phage with the ability of lysing some strains of MDR Klebsiella pneumoniae (vB_Kpn_3) was isolated from hospitals' wastewater and then characterized morphologically and genetically. Transmission electron microscopy and genetic analyses have revealed that vB_Kpn_3 is a member of Siphoviridae family. One-step growth curve also showed a burst time of 35 min and a burst size of 31 PFU/ml. The genome of the phage is composed of 112,080 bp with 41.33% G + C content carrying 186 open reading frames. Conclusion: vB_Kpn_3 is a broad host range phage that infects MDR K. pneumoniae and some other species of Enterobacteriaceae such as Escherichia coli and Salmonella typhi. In addition, no antibiotic resistance and toxin genes were detected in its genome.
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Affiliation(s)
- Fatemeh Habibinava
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
| | - Mohammad Soleimani
- Department of Microbiology, Faculty of Medicine, AjA University of Medical Sciences, Tehran, Iran
| | - Salehe Sabouri
- Pharmaceutics Research Center, Institute of Neuropharmacology, Kerman University of Medical Sciences, Kerman, Iran
| | - Mohsen Zargar
- Department of Microbiology, Qom Branch, Islamic Azad University, Qom, Iran
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41
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Characterization of a novel Vibrio parahaemolyticus host-phage pair and antibacterial effect against the host. Arch Virol 2022; 167:531-544. [DOI: 10.1007/s00705-021-05278-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 09/06/2021] [Indexed: 11/25/2022]
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42
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Harada LK, Silva EC, Rossi FP, Cieza B, Oliveira TJ, Pereira C, Tomazetto G, Silva BB, Squina FM, Vila MM, Setubal JC, Ha T, da Silva AM, Balcão VM. Characterization and in vitro testing of newly isolated lytic bacteriophages for the biocontrol of Pseudomonas aeruginosa. Future Microbiol 2022; 17:111-141. [PMID: 34989245 DOI: 10.2217/fmb-2021-0027] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Aim: Two lytic phages were isolated using P. aeruginosa DSM19880 as host and fully characterized. Materials & methods: Phages were characterized physicochemically, biologically and genomically. Results & conclusion: Host range analysis revealed that the phages also infect some multidrug-resistant (MDR) P. aeruginosa clinical isolates. Increasing MOI from 1 to 1000 significantly increased phage efficiency and retarded bacteria regrowth, but phage ph0034 (reduction of 7.5 log CFU/ml) was more effective than phage ph0031 (reduction of 5.1 log CFU/ml) after 24 h. Both phages belong to Myoviridae family. Genome sequencing of phages ph0031 and ph0034 showed that they do not carry toxin, virulence, antibiotic resistance and integrase genes. The results obtained are highly relevant in the actual context of bacterial resistance to antibiotics.
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Affiliation(s)
- Liliam K Harada
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Erica C Silva
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Fernando Pn Rossi
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Basilio Cieza
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Thais J Oliveira
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Carla Pereira
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Geizecler Tomazetto
- Department of Engineering, Biological & Chemical Engineering Section (BCE), Aarhus University, Aarhus, Denmark
| | - Bianca B Silva
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Fabio M Squina
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - Marta Mdc Vila
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil
| | - João C Setubal
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Taekjip Ha
- Department of Biophysics & Biophysical Chemistry, Johns Hopkins University, Baltimore, MD, USA
| | - Aline M da Silva
- Department of Biochemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
| | - Victor M Balcão
- PhageLab - Laboratory of Biofilms & Bacteriophages, University of Sorocaba, Sorocaba/SP, Brazil.,Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
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43
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Lievens EJP, Spagnuolo M, Réveillon T, Becks L. Delayed Lysis Time at High Multiplicities of Particles in a Chlorovirus-Chlorella Interaction. Microbes Environ 2022; 37:ME22068. [PMID: 36529502 PMCID: PMC9763037 DOI: 10.1264/jsme2.me22068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
When viruses infect microbial cells, their phenotypes depend on the host's genotype and on the environmental conditions. Here we describe such an effect in laboratory strains of the chlorovirus PBCV-1 and its algal host Chlorella variabilis. We studied the growth of six virus isolates, and found that the mean lysis time was 1.34±0.05 times longer at multiplicity of particles (MOP) 10 than at MOP 1. We could not detect any associated changes in burst size. This is a novel plastic trait for chloroviruses, and we hypothesize that it is caused by our specific laboratory algae.
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Affiliation(s)
- Eva J. P. Lievens
- Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Mainaustraße 252, 78464 Konstanz, Germany, Corresponding author. E-mail: ; Tel: +49 7531 88–3532
| | - Manuela Spagnuolo
- Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Mainaustraße 252, 78464 Konstanz, Germany
| | - Tom Réveillon
- Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Mainaustraße 252, 78464 Konstanz, Germany
| | - Lutz Becks
- Aquatic Ecology and Evolution Group, Limnological Institute, University of Konstanz, Mainaustraße 252, 78464 Konstanz, Germany
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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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45
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Sobhy H, Soliman EA, Abd El-Tawab AA, Elhofy FI, Askora A, El-Nahas EM, Wareth G, Ahmed W. Isolation, Characterization, and Efficacy of Three Lytic Phages Infecting Multidrug-Resistant Salmonella Serovars from Poultry Farms in Egypt. ARCHIVES OF RAZI INSTITUTE 2021; 76:507-519. [PMID: 34824744 DOI: 10.22092/ari.2021.355760.1719] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 08/22/2021] [Indexed: 01/21/2023]
Abstract
Multidrug-resistant (MDR) Salmonella serovars are considered a significant threat to veterinary and public health. Developing new antimicrobial compounds that can treat the infection caused by these notorious pathogens is a big challenge. Bacteriophages can be adsorbed on and inhibit the growth of bacteria, providing optimal and promising alternatives to chemical antimicrobial compounds against foodborne pathogens due to their abundance in nature and high host specificity. The objective of the current study was to isolate and characterize new phages from poultry farms and sewage and to evaluate their efficacy against S. Enteritidis isolates. The study reports three lytic phages designated as ϕSET1, ϕSET2, and ϕSET3 isolated from poultry carcasses and sewage samples in Qalubiya governorate Egypt. The effectiveness of phages was evaluated against multidrug-resistant S. Enteritidis strains. Electron microscopy showed that these phages belong to the Siphoviridae family. Phages were tested against 13 bacterial strains to determine their host range. They could infect four S. Enteritidis and one S. Typhimurium; however, they did not infect other tested bacterial species, indicating their narrow infectivity. The bacteriophage's single-step growth curves revealed a latent period of 20 min for ϕSET1 and 30 min for ϕSET2 and ϕSET3. The isolated Salmonella phages prevented the growth of S. Enteritidis for up to 18 hrs. The findings revealed that Salmonella phages could be used as alternative natural antibacterial compounds to combat infection with MDR S. Enteritidis in the poultry industry and represent a step forward to using large panels of phages for eliminating Salmonella from the food chain.
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Affiliation(s)
- H Sobhy
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh PO Box 13736, Egypt
| | - E A Soliman
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh PO Box 13736, Egypt
| | - A A Abd El-Tawab
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh PO Box 13736, Egypt
| | - F I Elhofy
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh PO Box 13736, Egypt
| | - A Askora
- Department of Microbiology and Botany, Faculty of Science, Zagazig University, 44519, Zagazig, Egypt
| | - E M El-Nahas
- Department of Virology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh PO Box 13736, Egypt
| | - G Wareth
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh PO Box 13736, Egypt.,Friedrich-Loeffler-Institut, Institute of Bacterial Infections and Zoonoses, Naumburger Str. 96a, 07743 Jena, Germany
| | - W Ahmed
- Department of Bacteriology, Immunology, and Mycology, Faculty of Veterinary Medicine, Benha University, Moshtohor, Toukh PO Box 13736, Egypt
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Complete Genome Sequence of Salmonella enterica Bacteriophage PRF-SP1. Microbiol Resour Announc 2021; 10:e0096521. [PMID: 34817216 PMCID: PMC8612080 DOI: 10.1128/mra.00965-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We characterized the complete genome sequence of the lytic Salmonella enterica bacteriophage PRF-SP1, isolated from Penang National Park, a conserved rainforest in northern Malaysia. The novel phage species from the Autographiviridae family has a 39,966-bp double-stranded DNA (dsDNA) genome containing 49 protein-encoding genes and shares 90.96% similarity with Escherichia phage DY1.
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47
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Kumar P, Meghvansi MK, Kamboj DV. Isolation, phenotypic characterization and comparative genomic analysis of 2019SD1, a polyvalent enterobacteria phage. Sci Rep 2021; 11:22197. [PMID: 34772986 PMCID: PMC8590004 DOI: 10.1038/s41598-021-01419-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 10/25/2021] [Indexed: 11/09/2022] Open
Abstract
Shigella has the remarkable capability to acquire antibiotic resistance rapidly thereby posing a significant public health challenge for the effective treatment of dysentery (Shigellosis). The phage therapy has been proven as an effective alternative strategy for controlling Shigella infections. In this study, we illustrate the isolation and detailed characterization of a polyvalent phage 2019SD1, which demonstrates lytic activity against Shigella dysenteriae, Escherichia coli, Vibrio cholerae, Enterococcus saccharolyticus and Enterococcus faecium. The newly isolated phage 2019SD1 shows adsorption time < 6 min, a latent period of 20 min and burst size of 151 PFU per bacterial cell. 2019SD1 exhibits considerable stability in a wide pH range and survives an hour at 50 °C. Under transmission electron microscope, 2019SD1 shows an icosahedral capsid (60 nm dia) and a 140 nm long tail. Further, detailed bioinformatic analyses of whole genome sequence data obtained through Oxford Nanopore platform revealed that 2019SD1 belongs to genus Hanrivervirus of subfamily Tempevirinae under the family Drexlerviridae. The concatenated protein phylogeny of 2019SD1 with the members of Drexlerviridae taking four genes (DNA Primase, ATP Dependent DNA Helicase, Large Terminase Protein, and Portal Protein) using the maximum parsimony method also suggested that 2019SD1 formed a distinct clade with the closest match of the taxa belonging to the genus Hanrivervirus. The genome analysis data indicate the occurrence of putative tail fiber proteins and DNA methylation mechanism. In addition, 2019SD1 has a well-established anti-host defence system as suggested through identification of putative anti-CRISPR and anti-restriction endonuclease systems thereby also indicating its biocontrol potential.
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Affiliation(s)
- Prince Kumar
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- Regional Ayurveda Research Institute, Gwalior, Madhya Pradesh, 474009, India
| | - Mukesh K Meghvansi
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
- Bioprocess Technology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India
| | - D V Kamboj
- Biotechnology Division, Defence Research & Development Establishment, Gwalior, Madhya Pradesh, 474002, India.
- Defence Research Laboratory, Tezpur, Assam, 784001, India.
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48
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The lytic siphophage vB_StyS-LmqsSP1 reduces Salmonella Typhimurium isolates on chicken skin. Appl Environ Microbiol 2021; 87:e0142421. [PMID: 34586906 DOI: 10.1128/aem.01424-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Phage-based biocontrol of bacteria is considered as a natural approach to combat food-borne pathogens. Salmonella spp. are notifiable and highly prevalent pathogens that cause foodborne diseases globally. In this study, six bacteriophages were isolated and further characterized that infect food-derived Salmonella isolates from different meat sources. The siphovirus VB_StyS-LmqsSP1, which was isolated from a cow´s nasal swab, was further subjected to in-depth characterization. Phage-host interaction investigations in liquid medium showed that vB_StyS-LmqsSP1 can suppress the growth of Salmonella spp. isolates at 37°C for ten hours and reduce the bacterial titer at 4°C significantly. A reduction of 1.4 to 3 log units was observed in investigations with two food-derived Salmonella isolates and one reference strain under cooling conditions using MOIs of 104 and 105. Phage application on chicken skin resulted in a reduction of about 2 log units in the tested Salmonella isolates from the first three hours throughout a one-week experiment at cooling temperature and an MOI of 105. The one-step growth curve analysis using vB_StyS-LmqsSP1 demonstrated a 60-min latent period and a burst size of 50-61 PFU/infected cell for all tested hosts. Furthermore, the genome of the phage was determined to be free from genes causing undesired effects. Based on the phenotypic and genotypic properties, LmqsSP1 was assigned as a promising candidate for biocontrol of Salmonella Typhimurium in food. Importance: Salmonella enterica is one of the major global causes of foodborne enteritis in humans. The use of chemical sanitizers for reducing bacterial pathogens in the food chain can result in the spread of bacterial resistance. Targeted and clean label intervention strategies can reduce Salmonella contamination in food. The significance of our research demonstrates the suitability of a bacteriophage (vB_StyS-LmqsSP1) for biocontrol of Salmonella enterica serovar Typhimurium on poultry due to its lytic efficacy under conditions prevailing in food production environments.
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The Characterization of a Novel Phage, pPa_SNUABM_DT01, Infecting Pseudomonas aeruginosa. Microorganisms 2021; 9:microorganisms9102040. [PMID: 34683360 PMCID: PMC8541153 DOI: 10.3390/microorganisms9102040] [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: 08/16/2021] [Revised: 09/15/2021] [Accepted: 09/24/2021] [Indexed: 12/25/2022] Open
Abstract
The bacterial genus Pseudomonas is a common causative agent of infections in veterinary medicine. In this study, we focused on Pseudomonas aeruginosa canine otitis externa isolates. Due to prolonged antibiotic treatment of otitis externa, antibiotic resistance is common and has become a major complication. Many alternatives to antibiotics have been studied, with bacteriophages emerging as the most promising alternatives. Here, we isolated and characterized a novel phage, pPa_SNUABM_DT01, by investigating its morphology, growth, lysis kinetics, and genomic characteristics. Phages have a vigorous capacity to eliminate bacterial cells through bacterial lysis. This capacity is dependent on the multiplicity of infection (MOI), but even at low MOIs, the phage successfully inhibited bacterial regrowth. The phage genome was 265,520 bp in size and comprised 312 putative open reading frames (ORFs). Comparative genome analysis demonstrated that the phage is a novel species in Myoviridae. The nucleotide similarity was moderately high compared with the Pseudomonas virus, Noxifer. However, a phylogenetic analysis and a dot plot indicated that pPa_SNUABM_DT01 is not closely related to the Phikzvirus or Noxifervirus genus but, instead, belongs to a novel one. The genome comparisons also indicate that the phage, pPa_SNUABM_DT01, could be a novel genus.
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Manufacturing Bacteriophages (Part 1 of 2): Cell Line Development, Upstream, and Downstream Considerations. Pharmaceuticals (Basel) 2021; 14:ph14090934. [PMID: 34577634 PMCID: PMC8471501 DOI: 10.3390/ph14090934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 09/06/2021] [Accepted: 09/15/2021] [Indexed: 01/21/2023] Open
Abstract
Within this first part of the two-part series on phage manufacturing, we will give an overview of the process leading to bacteriophages as a drug substance, before covering the formulation into a drug product in the second part. The principal goal is to provide the reader with a comprehensive framework of the challenges and opportunities that present themselves when developing manufacturing processes for bacteriophage-based products. We will examine cell line development for manufacture, upstream and downstream processes, while also covering the additional opportunities that engineered bacteriophages present.
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