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Bayat F, Hilal A, Thirugnanasampanthar M, Tremblay D, Filipe CDM, Moineau S, Didar TF, Hosseinidoust Z. High throughput platform technology for rapid target identification in personalized phage therapy. Nat Commun 2024; 15:5626. [PMID: 38992046 PMCID: PMC11239838 DOI: 10.1038/s41467-024-49710-2] [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: 05/02/2023] [Accepted: 06/13/2024] [Indexed: 07/13/2024] Open
Abstract
As bacteriophages continue to gain regulatory approval for personalized human therapy against antibiotic-resistant infections, there is a need for transformative technologies for rapid target identification through multiple, large, decentralized therapeutic phages biobanks. Here, we design a high throughput phage screening platform comprised of a portable library of individual shelf-stable, ready-to-use phages, in all-inclusive solid tablets. Each tablet encapsulates one phage along with luciferin and luciferase enzyme stabilized in a sugar matrix comprised of pullulan and trehalose capable of directly detecting phage-mediated adenosine triphosphate (ATP) release through ATP bioluminescence reaction upon bacterial cell burst. The tablet composition also enhances desiccation tolerance of all components, which should allow easier and cheaper international transportation of phages and as a result, increased accessibility to therapeutic phages. We demonstrate high throughput screening by identifying target phages for select multidrug-resistant clinical isolates of Pseudomonas aeruginosa, Salmonella enterica, Escherichia coli, and Staphylococcus aureus with targets identified within 30-120 min.
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Affiliation(s)
- Fereshteh Bayat
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada
| | - Arwa Hilal
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada
| | | | - Denise Tremblay
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, QC, Canada
| | - Carlos D M Filipe
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, QC, Canada
- Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, QC, Canada
- Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, QC, Canada
| | - Tohid F Didar
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada.
- Department of Mechanical Engineering, McMaster University, Hamilton, Ontario, Canada.
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
| | - Zeinab Hosseinidoust
- School of Biomedical Engineering, McMaster University, Hamilton, Ontario, Canada.
- Department of Chemical Engineering, McMaster University, Hamilton, Ontario, Canada.
- Michael DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Ontario, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Ontario, Canada.
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2
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Zhang Y, Wang R, Hu Q, Lv N, Zhang L, Yang Z, Zhou Y, Wang X. Characterization of Pseudomonas aeruginosa bacteriophages and control hemorrhagic pneumonia on a mice model. Front Microbiol 2024; 15:1396774. [PMID: 38808279 PMCID: PMC11132263 DOI: 10.3389/fmicb.2024.1396774] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 04/12/2024] [Indexed: 05/30/2024] Open
Abstract
Pseudomonas aeruginosa is one of the most common pathogens causing hemorrhagic pneumonia in Chinese forest musk deer. Multidrug-resistant P. aeruginosa is frequently isolated from the lungs of affected musk deer in Shaanxi Province, China. With the increasing bacterial drug resistance, commonly used antibiotics have shown limited efficacy against drug-resistant P. aeruginosa. Therefore, phages have garnered attention as a promising alternative to antibiotics among researchers. In this study, phages vB_PaeP_YL1 and vB_PaeP_YL2 (respectively referred to as YL1 and YL2) were isolated from mixed sewage samples from a farm. YL1 and YL2 exhibit an icosahedral head and a non-contractile short tail, belonging to the Podoviridae family. Identification results demonstrate good tolerance to low temperatures and pH levels, with minimal variation in potency within 30 min of UV irradiation. The MOI for both YL1 and YL2 was 0.1, and their one-step growth curve latent periods were 10 min and 20 min, respectively. Moreover, both single phage and phage cocktail effectively inhibited the growth of the host bacteria in vitro, with the phage cocktail showing superior inhibitory effects compared to the single phage. YL1 and YL2 possess double-stranded DNA genomes, with YL1 having a genome size of 72,187 bp and a total G + C content of 55.02%, while YL2 has a genome size of 72,060 bp and a total G + C content of 54.98%. YL1 and YL2 are predicted to have 93 and 92 open reading frames (ORFs), respectively, and no ORFs related to drug resistance or lysogeny were found in both phages. Genome annotation and phylogenetic analysis revealed that YL1 is closely related to vB_PaeP_FBPa1 (ON857943), while YL2 is closely related to vB_PaeP_FBPa1 (ON857943) and Phage26 (NC041907). In a mouse model of hemorrhagic pneumonia, phage cocktail treatment showed better control of the disease and significantly reduced lung bacterial load compared to single phage treatment. Therefore, YL1 and YL2 have the potential for the prevention and treatment of multidrug-resistant P. aeruginosa infections.
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Affiliation(s)
- Yanjie Zhang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Ruiqing Wang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Qingxia Hu
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Ni Lv
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Likun Zhang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Zengqi Yang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Yefei Zhou
- Nanjing Xiao Zhuang University, Nanjing, China
| | - Xinglong Wang
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
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Martínez-Gallardo MJ, Villicaña C, Yocupicio-Monroy M, Alcaraz-Estrada SL, León-Félix J. Current knowledge in the use of bacteriophages to combat infections caused by Pseudomonas aeruginosa in cystic fibrosis. Folia Microbiol (Praha) 2023; 68:1-16. [PMID: 35931928 DOI: 10.1007/s12223-022-00990-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 07/02/2022] [Indexed: 11/04/2022]
Abstract
Pseudomonas aeruginosa (PA) is considered the first causal agent of morbidity and mortality in people with cystic fibrosis (CF) disease. Multi-resistant strains have emerged due to prolonged treatment with specific antibiotics, so new alternatives have been sought for their control. In this context, there is a renewed interest in therapies based on bacteriophages (phages) supported by several studies suggesting that therapy based on lytic phages and biofilm degraders may be promising for the treatment of lung infections in CF patients. However, there is little clinical data about phage studies in CF and the effectiveness and safety in patients with this disease has not been clear. Therefore, studies regarding on phage characterization, selection, and evaluation in vitro and in vivo models will provide reliable information for designing effective cocktails, either using mixed phages or in combination with antibiotics, making a great progress in clinical research. Hence, this review focuses on the most relevant and recent findings on the activity of lytic phages against PA strains isolated from CF patients and hospital environments, and discusses perspectives on the use of phage therapy on the treatment of PA in CF patients.
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Affiliation(s)
- María José Martínez-Gallardo
- Laboratory of Molecular Biology and Functional Genomics, Centro de Investigación en Alimentación y Desarrollo, Culiacán, Sinaloa, A.C. (CIAD), Mexico
| | - Claudia Villicaña
- CONACYT-Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Culiacán, Sinaloa, Mexico
| | - Martha Yocupicio-Monroy
- Postgraduate in Genomic Sciences, Universidad Autónoma de la Ciudad de México (UACM), Mexico City, Mexico
| | | | - Josefina León-Félix
- Laboratory of Molecular Biology and Functional Genomics, Centro de Investigación en Alimentación y Desarrollo, Culiacán, Sinaloa, A.C. (CIAD), Mexico.
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Comparative Analysis of Novel Lytic Phages for Biological Control of Phytopathogenic Xanthomonas spp. Microbiol Spectr 2022; 10:e0296022. [PMID: 36326506 PMCID: PMC9769650 DOI: 10.1128/spectrum.02960-22] [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] [Indexed: 11/06/2022] Open
Abstract
Xanthomonas is an important genus of plant-pathogenic bacteria that affects agronomic and economically important crops, causing serious economic losses. In fact, several Xanthomonas species are considered regulated quarantine pests. Due to the lack of effective control measures to treat plant-pathogenic bacteria, innovative control tools are needed to carry out integrated disease management. In this regard, bacteriophages (phages), viruses of bacteria, constitute a promising biocontrol tool. In this work, we report the isolation and characterization of 11 novel Xanthomonas arboricola pv. juglandis phages belonging to different families and genera of the class Caudoviricetes. Infectivity matrix in more than 60 isolates of different xanthomonads and other phytopathogenic bacteria suggests that these phages are specific to the Xanthomonas genus, with different host ranges depending on the isolates tested. Interestingly, some of these phages showed relevant features to be used as biocontrol tools to combat pathogenic Xanthomonas spp. as important as X. oryzae or X. citri. IMPORTANCE Phytopathogenic bacteria represent serious losses worldwide. The lack of current treatments has focused the spotlight on phages, viruses of bacteria, as very promising biocontrol tools. Phages are very specific and can help to control bacterial infections in crops, as is the case of xanthomonads-associated diseases. The discovery of new environmental phages with lytic capacity that can help to combat these pathogens is of special relevance, and it is necessary to implement phage isolation and characterization techniques to determine their host range and their genomic properties. The establishment of phage collections worldwide will allow their use as preventive, diagnostic, or therapeutic tools. Although there is still a long way to go, this work is a step forward in the implementation of new ecofriendly techniques to combat key pathogens in the field.
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Abstract
Here, we describe genome sequences of 17 Pseudomonas aeruginosa phages, including therapeutic candidates. They belong to the families Myoviridae, Podoviridae, and Siphoviridae and six different genera. The genomes ranged in size from 42,788 to 88,805 bp, with G+C contents of 52.5% to 64.3%, and the numbers of coding sequences from 58 to 179. Here, we describe genome sequences of 17 Pseudomonas aeruginosa phages, including therapeutic candidates. They belong to the families Myoviridae, Podoviridae, and Siphoviridae and six different genera. The genomes ranged in size from 42,788 to 88,805 bp, with G+C contents of 52.5% to 64.3% and numbers of coding sequences from 58 to 179.
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Abstract
With the fast emergence of serious antibiotic resistance and the lagged discovery of novel antibacterial drugs, phage therapy for pathogenic bacterial infections has acquired great attention in the clinics. However, development of therapeutic phages also faces tough challenges, such as laborious screening and time to generate effective phage drugs since each phage may only lyse a narrow scope of bacterial strains. Identifying highly effective phages with broad host ranges is crucial for improving phage therapy. Here, we isolated and characterized several lytic phages from various environments specific for Pseudomonas aeruginosa by testing their growth, invasion, host ranges, and potential for killing targeted bacteria. Importantly, we identified several therapeutic phages (HX1, PPY9, and TH15) with broad host ranges to lyse laboratory strains and clinical isolates of P. aeruginosa with multi-drug resistance (MDR) both in vitro and in mouse models. In addition, we analyzed critical genetic traits related to the high-level broad host coverages by genome sequencing and subsequent computational analysis against known phages. Collectively, our findings establish that these novel phages may have potential for further development as therapeutic options for patients who fail to respond to conventional treatments.IMPORTANCE Novel lytic phages isolated from various environmental settings were systematically characterized for their critical genetic traits, morphology structures, host ranges against laboratory strains and clinical multi-drug resistant (MDR) Pseudomonas aeruginosa, and antibacterial capacity both in vitro and in mouse models. First, we characterized the genetic traits and compared with other existing phages. Furthermore, we utilized acute pneumonia induced by laboratorial strain PAO1, and W19, an MDR clinical isolate and chronic pneumonia by agar beads laden with FDR1, a mucoid phenotype strain isolated from the sputum of a cystic fibrosis (CF) patient. Consequently, we found that these phages not only suppress bacteria in vitro but also significantly reduce the infection symptom and disease progression in vivo, including lowered bug burdens, inflammatory responses and lung injury in mice, suggesting that they may be further developed as therapeutic agents against MDR P. aeruginosa.
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Bayat F, Maddiboina D, Didar TF, Hosseinidoust Z. Regenerating heavily biofouled dissolved oxygen sensors using bacterial viruses. RSC Adv 2021; 11:8346-8355. [PMID: 35423325 PMCID: PMC8695194 DOI: 10.1039/d0ra10156g] [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] [Received: 12/02/2020] [Accepted: 02/11/2021] [Indexed: 11/27/2022] Open
Abstract
Bacterial biofilms are aggregates of bacterial cells embedded in a self-produced extracellular polymeric matrix. Biofilm formation has always been considered a major challenge for sensors used in underwater measurements, and is a primary source of measurement error, especially when it comes to long-term in situ monitoring. We demonstrate the utility of lytic bacteriophages (bacterial viruses) as a non-invasive strategy for removing bacterial biofilms formed on the gas permeable membrane of electrochemical dissolved oxygen sensors. Our results show that a 4 day Pseudomonas aeruginosa biofilm with a fully developed matrix significantly affected the sensor signal and response time, decreasing the signal by 32% and increasing the response time by 94%. In addition, measurements with the biofouled membrane had a very low signal to nose ratio compared to a clean sensor membrane. A single dose of overnight phage treatment effectively removed the biofilm (as indicated by scanning electron micrographs and fluorescence images of the membrane), without the need for repeated treatments. Furthermore, the sensor signal that had plummeted by 32% for a fully biofouled membrane, was returned to the original value (7.96 ± 0.27 mg L−1) after phage treatment and the signal to noise ratio (calculated as the ratio of mean to standard deviation) increased 8 folds for a phage-treated membrane compared to a biofouled membrane. Our data indicate near complete regeneration and signal recovery for the dissolved oxygen sensor, making the biofouled sensor reusable without the use of harsh chemicals that could destroy the fragile sensor membrane. Lytic bacteriophages can be utilized as a non-invasive method for removing bacterial biofilms formed on the surface of gas permeable membranes of dissolved oxygen sensors.![]()
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Affiliation(s)
- Fereshteh Bayat
- School of Biomedical Engineering
- McMaster University
- Hamilton
- Canada
| | | | - Tohid F. Didar
- School of Biomedical Engineering
- McMaster University
- Hamilton
- Canada
- Department of Mechanical Engineering
| | - Zeinab Hosseinidoust
- School of Biomedical Engineering
- McMaster University
- Hamilton
- Canada
- Department of Chemical Engineering
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8
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Shi X, Zhao F, Sun H, Yu X, Zhang C, Liu W, Pan Q, Ren H. Characterization and Complete Genome Analysis of Pseudomonas aeruginosa Bacteriophage vB_PaeP_LP14 Belonging to Genus Litunavirus. Curr Microbiol 2020; 77:2465-2474. [PMID: 32367280 DOI: 10.1007/s00284-020-02011-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 04/24/2020] [Indexed: 12/17/2022]
Abstract
A lytic Pseudomonas aeruginosa phage vB_PaeP_LP14 belonging to the family Podoviridae was isolated from infected mink. The microbiological characterization revealed that LP14 was stable at 40 to 50 °C and stable over a broad range of pH (5 to 12). The latent period was 5 min, and the burst size was 785 pfu/infected cell. The whole-genome sequencing showed that LP14 was a dsDNA virus and has a genome of 73,080 bp. The genome contained 93 predicted open reading frames (ORFs), 17 of which have known functions including DNA replication and modification, transcriptional regulation, structural and packaging proteins, and host cell lysis. No tRNA genes were identified. BLASTn analysis revealed that phage LP14 had a high-sequence identity (96%) with P. aeruginosa phage YH6. Both morphological characterization and genome annotation indicate that phage LP14 is a memberof the family Podoviridae genus Litunavirus. The study of phage LP14 will provide basic information for further research on treatment of P. aeruginosa infections.
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Affiliation(s)
- Xiaojie Shi
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Feiyang Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Huzhi Sun
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Xiaoyan Yu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Qiang Pan
- Qingdao Phagepharm Bio-tech Co, Ltd, Qingdao, Shandong, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, Shandong, China.
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9
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RLP, a bacteriophage of the family Podoviridae, rescues mice from bacteremia caused by multi-drug-resistant Pseudomonas aeruginosa. Arch Virol 2020; 165:1289-1297. [DOI: 10.1007/s00705-020-04601-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 02/28/2020] [Indexed: 02/01/2023]
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10
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Yu X, Xu Y, Gu Y, Zhu Y, Liu X. Characterization and genomic study of "phiKMV-Like" phage PAXYB1 infecting Pseudomonas aeruginosa. Sci Rep 2017; 7:13068. [PMID: 29026171 PMCID: PMC5638911 DOI: 10.1038/s41598-017-13363-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 09/21/2017] [Indexed: 12/13/2022] Open
Abstract
Bacteriophage PAXYB1 was recently isolated from wastewater samples. This phage was chosen based on its lytic properties against clinical isolates of Pseudomonas aeruginosa (P. aeruginosa). In the present study, characterized PAXYB1, clarified its morphological and lytic properties, and analyzed its complete genome sequence. Based on the morphology of PAXYB1, it is a Podoviridae. The linear GC-rich (62.29%) double-stranded DNA genome of PAXYB1 is 43,337 bp including direct terminal repeats (DTRs) of 468 bp. It contains 60 open reading frames (ORFs) that are all encoded within the same strand. We also showed that PAXYB1 is a virulent phage and a new member of the phiKMV-like phages genus. Twenty-eight out of sixty predicted gene products (gps) showed significant homology to proteins of known function, which were confirmed by analyzing the structural proteome. Altogether, our work identified a novel lytic bacteriophage that lyses P. aeruginosa PAO1 and efficiently infects and kills several clinical isolates of P. aeruginosa. This phage has potential for development as a biological disinfectant to control P. aeruginosa infections.
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Affiliation(s)
- Xinyan Yu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, 211166, China
| | - Yue Xu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, 211166, China
| | - Yu Gu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, 211166, China
| | - Yefei Zhu
- The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xiaoqiu Liu
- Key Laboratory of Pathogen Biology of Jiangsu Province, Department of Microbiology, Nanjing Medical University, Nanjing, 211166, China.
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11
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Nogueira F, Karumidze N, Kusradze I, Goderdzishvili M, Teixeira P, Gouveia IC. Immobilization of bacteriophage in wound-dressing nanostructure. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2017; 13:2475-2484. [PMID: 28842374 DOI: 10.1016/j.nano.2017.08.008] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2017] [Revised: 08/03/2017] [Accepted: 08/09/2017] [Indexed: 12/27/2022]
Abstract
Opportunistic bacteria that cause life-threatening infections are still a central problem associated with a healthcare setting. Bacteriophage capsid immobilization on nanostructured polymers maximizes its tail exposure and looks promising in applications toward skin-infections as alternative to antibiotics standardly used. The main goal of this work was to investigate the covalent immobilization of vB_Pae_Kakheti25 bacteriophage capsid on polycaprolactone (PCL) nanofibers (non-woven textile), as a potential effective antimicrobial, laundry resistant and non-toxic dressing for biomedical use. Surface analyses showed that the immobilization of vB_Pae_Kakheti25 bacteriophage capsid on PCL nanofibres oriented bacteriophage tails to interact with bacteria. Furthermore, antimicrobial assays showed a very effective 6 log bacterial reduction, which was equivalent to 99.9999%, after immediate and 2 hours of contact, even following 25 washing cycles (due to covalent bond). The activity of PCL-vB_Pae_Kakheti25 against P. aeruginosa was immediate and its reduction was complete.
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Affiliation(s)
- Frederico Nogueira
- CICS-UBI - Health Sciences Research Centre, University of Beira Interior, Portugal; FibEnTech - Fiber Materials and Environmental Technologies, University of Beira Interior, Portugal
| | - Natia Karumidze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
| | - Ia Kusradze
- G. Eliava Institute of Bacteriophages, Microbiology and Virology, Tbilisi, Georgia
| | | | - Pilar Teixeira
- Institute for Biotechnology and Bioengineering (IBB), Portugal
| | - Isabel C Gouveia
- FibEnTech - Fiber Materials and Environmental Technologies, University of Beira Interior, Portugal.
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12
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Van Belleghem JD, Clement F, Merabishvili M, Lavigne R, Vaneechoutte M. Pro- and anti-inflammatory responses of peripheral blood mononuclear cells induced by Staphylococcus aureus and Pseudomonas aeruginosa phages. Sci Rep 2017; 7:8004. [PMID: 28808331 PMCID: PMC5556114 DOI: 10.1038/s41598-017-08336-9] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 07/07/2017] [Indexed: 12/30/2022] Open
Abstract
The ability of bacteriophages to kill bacteria is well known, as is their potential use as alternatives to antibiotics. As such, bacteriophages reach high doses locally through infection of their bacterial host in the human body. In this study we assessed the gene expression profile of peripheral blood monocytes from six donors for twelve immunity-related genes (i.e. CD14, CXCL1, CXCL5, IL1A, IL1B, IL1RN, IL6, IL10, LYZ, SOCS3, TGFBI and TNFA) induced by Staphylococcus aureus phage ISP and four Pseudomonas aeruginosa phages (i.e. PNM, LUZ19, 14-1 and GE-vB_Pae-Kakheti25). The phages were able to induce clear and reproducible immune responses. Moreover, the overall immune response was very comparable for all five phages: down-regulation of LYZ and TGFBI, and up-regulation of CXCL1, CXCL5, IL1A, IL1B, IL1RN, IL6, SOCS3 and TNFA. The observed immune response was shown to be endotoxin-independent and predominantly anti-inflammatory. Addition of endotoxins to the highly purified phages did not cause an immune response comparable to the one induced by the (endotoxin containing) phage lysate. In addition, the use of an intermediate level of endotoxins tipped the immune response to a more anti-inflammatory response, i.e. up-regulation of IL1RN and a strongly reduced expression of CXCL1 and CXCL5.
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Affiliation(s)
- Jonas D Van Belleghem
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, University Ghent, Medical Research Building II, De Pintelaan 185, 9000, Ghent, Belgium.
| | - Frédéric Clement
- Center for Vaccinology, Ghent University Hospital, Ghent, Belgium
| | - Maya Merabishvili
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, University Ghent, Medical Research Building II, De Pintelaan 185, 9000, Ghent, Belgium
- Laboratory for Molecular and Cellular Technology (LabMCT) Queen Astrid Military Hospital, Bruynstraat 1, 1120, Brussels, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, KULeuven, Kasteelpark Arenberg 21 box 2462, 3001, Leuven, Belgium
| | - Mario Vaneechoutte
- Laboratory Bacteriology Research, Department of Clinical Chemistry, Microbiology and Immunology, University Ghent, Medical Research Building II, De Pintelaan 185, 9000, Ghent, Belgium
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13
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Flores V, Sepúlveda-Robles O, Cazares A, Kameyama L, Guarneros G. Comparative genomic analysis of Pseudomonas aeruginosa phage PaMx25 reveals a novel siphovirus group related to phages infecting hosts of different taxonomic classes. Arch Virol 2017; 162:2345-2355. [PMID: 28462462 DOI: 10.1007/s00705-017-3366-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 03/12/2017] [Indexed: 12/20/2022]
Abstract
Bacteriophages (phages) are estimated to be the most abundant and diverse entities in the biosphere harboring vast amounts of novel genetic information. Despite the genetic diversity observed, many phages share common features, such as virion morphology, genome size and organization, and can readily be associated with clearly defined phage groups. However, other phages display unique genomes or, alternatively, mosaic genomes composed of regions that share homology with those of phages of diverse origins; thus, their relationships cannot be easily assessed. In this work, we present a functional and comparative genomic analysis of Pseudomonas aeruginosa phage PaMx25, a virulent member of the Siphoviridae family. The genomes of PaMx25 and a highly homologous phage NP1, bore sequence homology and synteny with the genomes of phages that infect hosts different than Pseudomonas. In order to understand the relationship of the PaMx25 genome with that of other phages, we employed several computational approaches. We found that PaMx25 and NP1 effectively bridged several phage groups. It is expected that as more phage genomes become available, more gaps will be filled, blurring the boundaries that currently separate phage groups.
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Affiliation(s)
- Víctor Flores
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico
| | - Omar Sepúlveda-Robles
- Catedrático CONACyT - Coordinación de Investigación en Salud, Instituto Mexicano del Seguro Social (IMSS), Centro Médico Nacional Siglo XXI, Mexico City, Mexico
| | - Adrián Cazares
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico
| | - Luis Kameyama
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico
| | - Gabriel Guarneros
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City, Mexico.
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Turner D, Wand ME, Briers Y, Lavigne R, Sutton JM, Reynolds DM. Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB_AbaS_Loki. PLoS One 2017; 12:e0172303. [PMID: 28207864 PMCID: PMC5313236 DOI: 10.1371/journal.pone.0172303] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/02/2017] [Indexed: 01/17/2023] Open
Abstract
Acinetobacter baumannii has emerged as an important nosocomial pathogen in healthcare and community settings. While over 100 of Acinetobacter phages have been described in the literature, relatively few have been sequenced. This work describes the characterisation and genome annotation of a new lytic Acinetobacter siphovirus, vB_AbaS_Loki, isolated from activated sewage sludge. Sequencing revealed that Loki encapsulates a 41,308 bp genome, encoding 51 predicted open reading frames. Loki is most closely related to Acinetobacter phage IME_AB3 and more distantly related to Burkholderia phage KL1, Paracoccus phage vB_PmaS_IMEP1 and Pseudomonas phages vB_Pae_Kakheti25, vB_PaeS_SCH_Ab26 and PA73. Loki is characterised by a narrow host range, among the 40 Acinetobacter isolates tested, productive infection was only observed for the propagating host, A. baumannii ATCC 17978. Plaque formation was found to be dependent upon the presence of Ca2+ ions and adsorption to host cells was abolished upon incubation with a mutant of ATCC 17978 encoding a premature stop codon in lpxA. The complete genome sequence of vB_AbaS_Loki was deposited in the European Nucleotide Archive (ENA) under the accession number LN890663.
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Affiliation(s)
- Dann Turner
- Centre for Research in Biosciences, Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, United Kingdom
| | - Matthew E. Wand
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Applied Biosciences, Ghent University, Ghent, Belgium
- Laboratory of Gene Technology, Biosystems Department, KU Leuven, Heverlee, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Biosystems Department, KU Leuven, Heverlee, Belgium
| | - J. Mark Sutton
- National Infections Service, Public Health England, Porton Down, Salisbury, Wiltshire, United Kingdom
| | - Darren M. Reynolds
- Centre for Research in Biosciences, Department of Applied Sciences, Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, United Kingdom
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15
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Van Belleghem JD, Merabishvili M, Vergauwen B, Lavigne R, Vaneechoutte M. A comparative study of different strategies for removal of endotoxins from bacteriophage preparations. J Microbiol Methods 2017; 132:153-159. [DOI: 10.1016/j.mimet.2016.11.020] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Revised: 11/28/2016] [Accepted: 11/28/2016] [Indexed: 01/26/2023]
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16
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Holmfeldt K, Solonenko N, Howard-Varona C, Moreno M, Malmstrom RR, Blow MJ, Sullivan MB. Large-scale maps of variable infection efficiencies in aquatic Bacteroidetes phage-host model systems. Environ Microbiol 2016; 18:3949-3961. [PMID: 27235779 DOI: 10.1111/1462-2920.13392] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Accepted: 05/21/2015] [Indexed: 01/21/2023]
Abstract
Microbes drive ecosystem functioning and their viruses modulate these impacts through mortality, gene transfer and metabolic reprogramming. Despite the importance of virus-host interactions and likely variable infection efficiencies of individual phages across hosts, such variability is seldom quantified. Here, we quantify infection efficiencies of 38 phages against 19 host strains in aquatic Cellulophaga (Bacteroidetes) phage-host model systems. Binary data revealed that some phages infected only one strain while others infected 17, whereas quantitative data revealed that efficiency of infection could vary 10 orders of magnitude, even among phages within one population. This provides a baseline for understanding and modeling intrapopulation host range variation. Genera specific host ranges were also informative. For example, the Cellulophaga Microviridae, showed a markedly broader intra-species host range than previously observed in Escherichia coli systems. Further, one phage genus, Cba41, was examined to investigate nonheritable changes in plating efficiency and burst size that depended on which host strain it most recently infected. While consistent with host modification of phage DNA, no differences in nucleotide sequence or DNA modifications were detected, leaving the observation repeatable, but the mechanism unresolved. Overall, this study highlights the importance of quantitatively considering replication variations in studies of phage-host interactions.
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Affiliation(s)
- Karin Holmfeldt
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA.,Department of Biology and Environmental Sciences, Centre for Ecology and Evolution in Microbial Model Systems, Linnaeus University, Kalmar, Sweden
| | - Natalie Solonenko
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | - Mario Moreno
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
| | | | | | - Matthew B Sullivan
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
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17
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Gu J, Li X, Yang M, Du C, Cui Z, Gong P, Xia F, Song J, Zhang L, Li J, Yu C, Sun C, Feng X, Lei L, Han W. Therapeutic effect of Pseudomonas aeruginosa phage YH30 on mink hemorrhagic pneumonia. Vet Microbiol 2016; 190:5-11. [PMID: 27283850 DOI: 10.1016/j.vetmic.2016.03.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 03/11/2016] [Accepted: 03/25/2016] [Indexed: 10/22/2022]
Abstract
Hemorrhagic pneumonia caused by Pseudomonas aeruginosa remains one of the most costly infectious diseases among farmed mink and commonly leads to large economic losses during mink production. The objective of this study was to investigate the potential of using phages as a therapy against hemorrhagic pneumonia in mink. A broad-host-range phage from the Podoviridae family, YH30, was isolated using the mink-originating P. aeruginosa (serotype G) D7 strain as a host. The genome of YH30 was 72,192bp (54.92% G+C), contained 86 open reading frames and lacked regions encoding known virulence factors, integration-related proteins or antibiotic resistance determinants. These characteristics make YH30 eligible for use in phage therapy. The results of a curative treatment experiment demonstrated that a single intranasal administration of YH30 was sufficient to cure hemorrhagic pneumonia in mink. The mean colony count of P. aeruginosa in the blood and lung of YH30-protected mink was less than 10(3) CFU/mL (g) within 24h of bacterial challenge and ultimately became undetectable, whereas that in unprotected mink reached more than 10(8) CFU/mL (g). Additionally, YH30 dramatically improved the pathological manifestations of lung injury in mink with hemorrhagic pneumonia. Our work demonstrates the potential of phages to treat P. aeruginosa-caused hemorrhagic pneumonia in mink.
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Affiliation(s)
- Jingmin Gu
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Xinwei Li
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Mei Yang
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Chongtao Du
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Ziyin Cui
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Pengjuan Gong
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Feifei Xia
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Jun Song
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Lei Zhang
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Juecheng Li
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Chuang Yu
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Changjiang Sun
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Xin Feng
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Liancheng Lei
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China
| | - Wenyu Han
- College of Veterinary Medicine, Jilin University, Changchun 130062, PR China; Jiangsu Co-innovation Center for the Prevention and Control of important Animal Infectious Disease and Zoonoses, Yangzhou 225009, PR China.
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18
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Peters DL, Lynch KH, Stothard P, Dennis JJ. The isolation and characterization of two Stenotrophomonas maltophilia bacteriophages capable of cross-taxonomic order infectivity. BMC Genomics 2015; 16:664. [PMID: 26335566 PMCID: PMC4559383 DOI: 10.1186/s12864-015-1848-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 08/14/2015] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND A rapid worldwide increase in the number of human infections caused by the extremely antibiotic resistant bacterium Stenotrophomonas maltophilia is prompting alarm. One potential treatment solution to the current antibiotic resistance dilemma is "phage therapy", the clinical application of bacteriophages to selectively kill bacteria. RESULTS Towards that end, phages DLP1 and DLP2 (vB_SmaS-DLP_1 and vB_SmaS-DLP_2, respectively) were isolated against S. maltophilia strain D1585. Host range analysis for each phage was conducted using 27 clinical S. maltophilia isolates and 11 Pseudomonas aeruginosa strains. Both phages exhibit unusually broad host ranges capable of infecting bacteria across taxonomic orders. Transmission electron microscopy of the phage DLP1 and DLP2 morphology reveals that they belong to the Siphoviridae family of bacteriophages. Restriction fragment length polymorphism analysis and complete genome sequencing and analysis indicates that phages DLP1 and DLP2 are closely related but different phages, sharing 96.7 % identity over 97.2 % of their genomes. These two phages are also related to P. aeruginosa phages vB_Pae-Kakheti_25 (PA25), PA73, and vB_PaeS_SCH_Ab26 (Ab26) and more distantly related to Burkholderia cepacia complex phage KL1, which together make up a taxonomic sub-family. Phages DLP1 and DLP2 exhibited significant differences in host ranges and growth kinetics. CONCLUSIONS The isolation and characterization of phages able to infect two completely different species of bacteria is an exciting discovery, as phages typically can only infect related bacterial species, and rarely infect bacteria across taxonomic families, let alone across taxonomic orders.
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Affiliation(s)
- Danielle L Peters
- Department of Biological Sciences, 6-065 Centennial Centre for Interdisciplinary Science, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
| | - Karlene H Lynch
- Department of Biological Sciences, 6-065 Centennial Centre for Interdisciplinary Science, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 1400 College Plaza, Edmonton, AB, T6G 2C8, Canada.
| | - Jonathan J Dennis
- Department of Biological Sciences, 6-065 Centennial Centre for Interdisciplinary Science, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
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19
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Essoh C, Latino L, Midoux C, Blouin Y, Loukou G, Nguetta SPA, Lathro S, Cablanmian A, Kouassi AK, Vergnaud G, Pourcel C. Investigation of a Large Collection of Pseudomonas aeruginosa Bacteriophages Collected from a Single Environmental Source in Abidjan, Côte d'Ivoire. PLoS One 2015; 10:e0130548. [PMID: 26115051 PMCID: PMC4482731 DOI: 10.1371/journal.pone.0130548] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 05/22/2015] [Indexed: 12/12/2022] Open
Abstract
Twenty two distinct bacteriophages were isolated from sewage water from five locations in the city of Abidjan, Côte d'Ivoire over a two-year period, using a collection of Pseudomonas aeruginosa strains with diverse genotypes. The phages were characterized by their virulence spectrum on a panel of selected P. aeruginosa strains from cystic fibrosis patients and by whole genome sequencing. Twelve virions representing the observed diversity were visualised by electron microscopy. The combined observations showed that 17 phages, distributed into seven genera, were virulent, and that five phages were related to temperate phages belonging to three genera. Some showed similarity with known phages only at the protein level. The vast majority of the genetic variations among virulent phages from the same genus resulted from seemingly non-random horizontal transfer events, inside a population of P. aeruginosa phages with limited diversity. This suggests the existence of a single environmental reservoir or ecotype in which continuous selection is taking place. In contrast, mostly point mutations were observed among phages potentially capable of lysogenisation. This is the first study of P. aeruginosa phage diversity in an African city and it shows that a large variety of phage species can be recovered in a limited geographical site at least when different bacterial strains are used. The relative temporal and spatial stability of the Abidjan phage population might reflect equilibrium in the microbial community from which they are released.
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Affiliation(s)
- Christiane Essoh
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Libera Latino
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Cédric Midoux
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Yann Blouin
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Guillaume Loukou
- Laboratoire National de Santé Publique, Abidjan, Côte d’Ivoire
- Laboratoire de Bactériologie-Virologie, département de Sciences pharmaceutiques et Biologiques, Univ Félix Houphouët-Boigny, Abidjan, Côte d’Ivoire
| | - Simon-Pierre A. Nguetta
- Laboratoire de Génétique, Département des Biosciences, Univ Félix Houphouet-Boigny, Abidjan, Côte d’Ivoire
| | - Serge Lathro
- Laboratoire National de Santé Publique, Abidjan, Côte d’Ivoire
| | | | | | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France
- ENSTA ParisTech, Université Paris-Saclay, Palaiseau, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell, CEA, CNRS, Univ Paris-Sud, Université Paris-Saclay, Orsay, France
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20
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Abstract
Bacteria Pseudomonas aeruginosa, being opportunistic pathogens, are the major cause of nosocomial infections and, in some cases, the primary cause of death. They are virtually untreatable with currently known antibiotics. Phage therapy is considered as one of the possible approaches to the treatment of P. aeruginosa infections. Difficulties in the implementation of phage therapy in medical practice are related, for example, to the insufficient number and diversity of virulent phages that are active against P. aeruginosa. Results of interaction of therapeutic phages with bacteria in different conditions and environments are studied insufficiently. A little is known about possible interactions of therapeutic phages with resident prophages and plasmids in clinical strains in the foci of infections. This chapter highlights the different approaches to solving these problems and possible ways to expand the diversity of therapeutic P. aeruginosa phages and organizational arrangements (as banks of phages) to ensure long-term use of phages in the treatment of P. aeruginosa infections.
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Affiliation(s)
- Victor N Krylov
- Mechnikov Research Institute for Vaccines & Sera, Russian Academy of Medical Sciences, Moscow, Russia.
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21
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Kwiatek M, Mizak L, Parasion S, Gryko R, Olender A, Niemcewicz M. Characterization of five newly isolated bacteriophages active against Pseudomonas aeruginosa clinical strains. Folia Microbiol (Praha) 2014; 60:7-14. [PMID: 24993480 DOI: 10.1007/s12223-014-0333-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 06/24/2014] [Indexed: 12/19/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that causes serious infections, especially in patients with immunodeficiency. It exhibits multiple mechanisms of resistance, including efflux pumps, antibiotic modifying enzymes and limited membrane permeability. The primary reason for the development of novel therapeutics for P. aeruginosa infections is the declining efficacy of conventional antibiotic therapy. These clinical problems caused a revitalization of interest in bacteriophages, which are highly specific and have very effective antibacterial activity as well as several other advantages over traditional antimicrobial agents. Above all, so far, no serious or irreversible side effects of phage therapy have been described. Five newly purified P. aeruginosa phages named vB_PaeM_WP1, vB_PaeM_WP2, vB_PaeM_WP3, vB_PaeM_WP4 and vB_PaeP_WP5 have been characterized as potential candidates for use in phage therapy. They are representatives of the Myoviridae and Podoviridae families. Their host range, genome size, structural proteins and stability in various physical and chemical conditions were tested. The results of these preliminary investigations indicate that the newly isolated bacteriophages may be considered for use in phagotherapy.
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Affiliation(s)
- Magdalena Kwiatek
- Biological Threat Identification and Countermeasure Centre, Military Institute of Hygiene and Epidemiology, Lubelska 2, 24-100, Puławy, Poland,
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22
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Genome Analysis of Pseudomonas aeruginosa Bacteriophage KPP23, Belonging to the Family Siphoviridae. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00233-14. [PMID: 24855291 PMCID: PMC4031330 DOI: 10.1128/genomea.00233-14] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Bacteriophage (phage) therapy is expected to become an alternative therapy for Pseudomonas aeruginosa infections. P. aeruginosa phage KPP23 is a newly isolated phage belonging to the family Siphoviridae and may be a therapeutic phage candidate. We report its complete genome, which comprises 62,774 bp of double-stranded DNA containing 95 open reading frames.
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23
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Holmfeldt K, Howard-Varona C, Solonenko N, Sullivan MB. Contrasting genomic patterns and infection strategies of two co-existing Bacteroidetes podovirus genera. Environ Microbiol 2014; 16:2501-13. [PMID: 24428166 DOI: 10.1111/1462-2920.12391] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2013] [Accepted: 12/31/2013] [Indexed: 11/28/2022]
Abstract
Bacterial viruses (phages) are abundant, ecologically important biological entities. However, our understanding of their impact is limited by model systems that are primarily not well represented in nature, e.g. Enterophages and their hosts. Here, we investigate genomic characteristics and infection strategies among six aquatic Bacteroidetes phages that represent two genera of exceptionally large (∼70-75 kb genome) podoviruses, which were isolated from the same seawater sample using Cellulophaga baltica as host. Quantitative host range studies reveal that these genera have contrasting narrow (specialist) and broad (generalist) host ranges, with one-step growth curves revealing reduced burst sizes for the generalist phages. Genomic comparisons suggest candidate genes in each genus that might explain this host range variation, as well as provide hypotheses about receptors in the hosts. One generalist phage, φ38:1, was more deeply characterized, as its infection strategy switched from lytic on its original host to either inefficient lytic or lysogenic on an alternative host. If lysogenic, this phage was maintained extrachromosomally in the alternative host and could not be induced by mitomycin C. This work provides fundamental knowledge regarding phage-host ranges and their genomic drivers while also exploring the 'host environment' as a driver for switching phage replication mode.
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Affiliation(s)
- Karin Holmfeldt
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
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24
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Keen EC. Tradeoffs in bacteriophage life histories. BACTERIOPHAGE 2014; 4:e28365. [PMID: 24616839 PMCID: PMC3942329 DOI: 10.4161/bact.28365] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Revised: 02/24/2014] [Accepted: 02/26/2014] [Indexed: 11/19/2022]
Abstract
Viruses are the most abundant biological entities on the planet, yet most classical principles of evolutionary biology and ecology were not developed with viruses in mind. Here, the concept of biological tradeoffs, a fundamental tenet of life history theory, is examined in the context of bacteriophage biology. Specifically, several important parameters of phage life histories-replication, persistence, host range, and adsorption-are evaluated for tradeoffs. Available data indicate that replication rate is strongly negatively correlated with both persistence and host range, suggesting that the well-documented tradeoff in macroorganisms between offspring production and offspring quality also applies to phages. The biological tradeoffs that appear to characterize viruses' life histories have potential importance for viral evolution, ecology, and pathogenesis.
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Affiliation(s)
- Eric C Keen
- Department of Biology; University of Miami; Coral Gables, FL USA
- Laboratory of Molecular Biology; Center for Cancer Research; National Cancer Institute; National Institutes of Health; Bethesda, MD USA
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25
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Essoh C, Blouin Y, Loukou G, Cablanmian A, Lathro S, Kutter E, Thien HV, Vergnaud G, Pourcel C. The susceptibility of Pseudomonas aeruginosa strains from cystic fibrosis patients to bacteriophages. PLoS One 2013; 8:e60575. [PMID: 23637754 PMCID: PMC3634792 DOI: 10.1371/journal.pone.0060575] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Accepted: 02/28/2013] [Indexed: 01/21/2023] Open
Abstract
Phage therapy may become a complement to antibiotics in the treatment of chronic Pseudomonas aeruginosa infection. To design efficient therapeutic cocktails, the genetic diversity of the species and the spectrum of susceptibility to bacteriophages must be investigated. Bacterial strains showing high levels of phage resistance need to be identified in order to decipher the underlying mechanisms. Here we have selected genetically diverse P. aeruginosa strains from cystic fibrosis patients and tested their susceptibility to a large collection of phages. Based on plaque morphology and restriction profiles, six different phages were purified from "pyophage", a commercial cocktail directed against five different bacterial species, including P. aeruginosa. Characterization of these phages by electron microscopy and sequencing of genome fragments showed that they belong to 4 different genera. Among 47 P. aeruginosa strains, 13 were not lysed by any of the isolated phages individually or by pyophage. We isolated two new phages that could lyse some of these strains, and their genomes were sequenced. The presence/absence of a CRISPR-Cas system (Clustered Regularly Interspaced Short Palindromic Repeats and Crisper associated genes) was investigated to evaluate the role of the system in phage resistance. Altogether, the results show that some P. aeruginosa strains cannot support the growth of any of the tested phages belonging to 5 different genera, and suggest that the CRISPR-Cas system is not a major defence mechanism against these lytic phages.
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Affiliation(s)
- Christiane Essoh
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | - Yann Blouin
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
| | | | | | - Serge Lathro
- Laboratoire National de Santé Publique, Abidjan, Côte d'Ivoire
| | - Elizabeth Kutter
- The Evergreen State College, Olympia, Washington, United States of America
| | - Hoang Vu Thien
- Hôpital Armand Trousseau, Assistance Publique-Hôpitaux de Paris (APHP), Bactériologie, Paris, France
| | - Gilles Vergnaud
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
- DGA/MRIS- Mission pour la Recherche et l'Innovation Scientifique, Bagneux, France
| | - Christine Pourcel
- Univ Paris-Sud, Institut de Génétique et Microbiologie, UMR 8621, Orsay, France
- CNRS, Orsay, France
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26
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Turner D, Hezwani M, Nelson S, Salisbury V, Reynolds D. Characterization of the Salmonella bacteriophage vB_SenS-Ent1. J Gen Virol 2012; 93:2046-2056. [PMID: 22694898 DOI: 10.1099/vir.0.043331-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The bacteriophage vB_SenS-Ent1 (Ent1) is a member of the family Siphoviridae of tailed bacteriophages and infects a broad range of serovars of the enteric pathogen Salmonella enterica. The virion particle is composed of an icosahedral head 64 nm in diameter and a flexible, non-contractile tail of 116 × 8.5 nm possessing terminal fibres. The adsorption rate constant at 37 °C is 6.73 × 10(-9) ml min(-1). Latent and eclipse periods are 25 and 20 min, respectively, and the burst size is 35 progeny particles per cell after 35 min at 37 °C. Sequencing revealed a circularly permuted, 42 391 bp dsDNA genome containing 58 ORFs organized into four major transcriptional units. Comparisons with the genome sequences of other bacteriophages revealed a high level of nucleotide sequence identity and shared orthologous proteins with the Salmonella phages SETP3, SE2 and KS7 (SS3e) and the Escherichia phages K1G, K1H, K1ind1 and K1ind3.
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Affiliation(s)
- Dann Turner
- Centre for Research in Biosciences, Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Mohammed Hezwani
- Centre for Research in Biosciences, Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Shona Nelson
- Centre for Research in Biosciences, Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Vyv Salisbury
- Centre for Research in Biosciences, Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK
| | - Darren Reynolds
- Centre for Research in Biosciences, Department of Applied Sciences, University of the West of England, Coldharbour Lane, Bristol BS16 1QY, UK
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